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83 ++++-- v0.1.6/reference/sampleVarSpecServer.html | 86 ++++-- .../teal.modules.hermes-package.html | 91 ++++-- v0.1.6/reference/tm_g_barplot.html | 89 ++++-- v0.1.6/reference/tm_g_boxplot.html | 89 ++++-- v0.1.6/reference/tm_g_forest_tte.html | 99 +++++-- v0.1.6/reference/tm_g_km.html | 99 +++++-- v0.1.6/reference/tm_g_pca.html | 89 ++++-- v0.1.6/reference/tm_g_quality.html | 89 ++++-- v0.1.6/reference/tm_g_scatterplot.html | 89 ++++-- v0.1.6/reference/tm_g_volcanoplot.html | 89 ++++-- v0.1.6/reference/top_gene_plot.html | 80 ++++-- v0.1.6/reference/validate_gene_spec.html | 74 +++-- v0.1.6/reference/validate_n_levels.html | 74 +++-- 329 files changed, 19263 insertions(+), 8293 deletions(-) diff --git a/404.html b/404.html index 4a6ae41c..10cf0326 100644 --- a/404.html +++ b/404.html @@ -1,5 +1,4 @@ - - + @@ -41,14 +40,15 @@ Changelog
  • -
    main + +
    + main latest-tag v0.1.6 v0.1.5 -v0.1.4
    • +v0.1.4 + + + + - + @@ -57,65 +77,80 @@
    -

    Our Pledge

    +

    Our Pledge +

    We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.

    We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.

    -

    Our Standards

    +

    Our Standards +

    Examples of behavior that contributes to a positive environment for our community include:

    -
    • Demonstrating empathy and kindness toward other people
      • +
        +
      • Demonstrating empathy and kindness toward other people
      • Being respectful of differing opinions, viewpoints, and experiences
      • Giving and gracefully accepting constructive feedback
      • Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
      • Focusing on what is best not just for us as individuals, but for the overall community
        • -

      Examples of unacceptable behavior include:

      -
      • The use of sexualized language or imagery, and sexual attention or advances of any kind
        • +
      +

      Examples of unacceptable behavior include:

      +
        +
      • The use of sexualized language or imagery, and sexual attention or advances of any kind
      • Trolling, insulting or derogatory comments, and personal or political attacks
      • Public or private harassment
      • Publishing others’ private information, such as a physical or email address, without their explicit permission
      • Other conduct which could reasonably be considered inappropriate in a professional setting
        • -
    + +
    -

    Enforcement Responsibilities

    +

    Enforcement Responsibilities +

    Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.

    Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.

    -

    Scope

    +

    Scope +

    This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.

    -

    Enforcement

    +

    Enforcement +

    Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at [INSERT CONTACT METHOD]. All complaints will be reviewed and investigated promptly and fairly.

    All community leaders are obligated to respect the privacy and security of the reporter of any incident.

    -

    Enforcement Guidelines

    +

    Enforcement Guidelines +

    Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:

    -

    1. Correction

    +

    1. Correction +

    Community Impact: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.

    Consequence: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.

    -

    2. Warning

    +

    2. Warning +

    Community Impact: A violation through a single incident or series of actions.

    Consequence: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.

    -

    3. Temporary Ban

    +

    3. Temporary Ban +

    Community Impact: A serious violation of community standards, including sustained inappropriate behavior.

    Consequence: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.

    -

    4. Permanent Ban

    +

    4. Permanent Ban +

    Community Impact: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.

    Consequence: A permanent ban from any sort of public interaction within the community.

    -

    Attribution

    +

    Attribution +

    This Code of Conduct is adapted from the Contributor Covenant, version 2.1, available at https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.

    Community Impact Guidelines were inspired by Mozilla’s code of conduct enforcement ladder.

    For answers to common questions about this code of conduct, see the FAQ at https://www.contributor-covenant.org/faq. Translations are available at https://www.contributor-covenant.org/translations.

    @@ -123,17 +158,19 @@

    Attribution

    + + + + - - + + diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 0f472e2e..e3308d73 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -1,8 +1,22 @@ - -Contribution Guidelines • teal.modules.hermes + + + + + + + Skip to contents @@ -18,32 +32,38 @@ + - + + - + @@ -59,7 +79,8 @@

    🙏 Thank you for taking the time to contribute!

    Your input is deeply valued, whether an issue, a pull request, or even feedback, regardless of size, content or scope.

    -

    Table of contents

    +

    Table of contents +

    👶 Getting started

    📔 Code of Conduct

    🗃 License

    @@ -70,38 +91,47 @@

    Table of contents❓ Questions

    -

    Getting started

    +

    Getting started +

    Please refer the project documentation for a brief introduction. Please also see other articles within the project documentation for additional information.

    -

    Code of Conduct

    +

    Code of Conduct +

    A Code of Conduct governs this project. Participants and contributors are expected to follow the rules outlined therein.

    -

    License

    +

    License +

    All your contributions will be covered by this project’s license.

    -

    Issues

    +

    Issues +

    We use GitHub to track issues, feature requests, and bugs. Before submitting a new issue, please check if the issue has already been reported. If the issue already exists, please upvote the existing issue 👍.

    For new feature requests, please elaborate on the context and the benefit the feature will have for users, developers, or other relevant personas.

    -

    Pull requests

    +

    Pull requests +

    -

    Github flow

    +

    Github flow +

    This repository uses the Github flow model for collaboration. To submit a pull request:

    -
    1. +
        +

      1. Create a branch.

        Please see the branch naming convention below. If you don’t have write access to this repository, please fork it.

      2. Make changes.

        Make sure your code:

        -
        • passes all checks imposed by GitHub Actions
          • +
            +
          • passes all checks imposed by GitHub Actions
          • is well documented
          • is well tested with unit tests sufficiently covering the changes introduced
            • -
          +
        +

      3. Create a pull request (PR).

        In the pull request description, please link the relevant issue (if any), provide a detailed description of the change, and include any assumptions.

        @@ -115,64 +145,78 @@

        Github flow -

        Branch naming convention

        +

        Branch naming convention +

        Suppose your changes are related to a current issue in the current project; please name your branch as follows: <issue_id>_<short_description>. Please use underscore (_) as a delimiter for word separation. For example, 420_fix_ui_bug would be a suitable branch name if your change is resolving and UI-related bug reported in issue number 420 in the current project.

        If your change affects multiple repositories, please name your branches as follows: <issue_id>_<issue_repo>_<short description>. For example, 69_awesomeproject_fix_spelling_error would reference issue 69 reported in project awesomeproject and aims to resolve one or more spelling errors in multiple (likely related) repositories.

    monorepo and staged.dependencies -

    + +

    Sometimes you might need to change upstream dependent package(s) to be able to submit a meaningful change. We are using staged.dependencies functionality to simulate a monorepo behavior. The dependency configuration is already specified in this project’s staged_dependencies.yaml file. You need to name the feature branches appropriately. This is the only exception from the branch naming convention described above.

    Please refer to the staged.dependencies package documentation for more details.

    -

    Recommended development environment & tools

    +

    Recommended development environment & tools +

    -

    R & package versions

    +

    R & package versions +

    We continuously test our packages against the newest R version along with the most recent dependencies from CRAN and BioConductor. We recommend that your working environment is also set up in the same way. You can find the details about the R version and packages used in the R CMD check GitHub Action execution log - there is a step that prints out the R sessionInfo().

    If you discover bugs on older R versions or with an older set of dependencies, please create the relevant bug reports.

    -

    pre-commit

    +

    +pre-commit +

    We highly recommend that you use the pre-commit tool combined with R hooks for pre-commit to execute some of the checks before committing and pushing your changes.

    Pre-commit hooks are already available in this repository’s .pre-commit-config.yaml file.

    -

    Style guide

    +

    Style guide +

    This repository follows the standard tidyverse style guide and uses lintr for lint checks. Customized lint configurations are available in this repository’s .lintr file.

    -

    Recognition model

    +

    Recognition model +

    As mentioned previously, all contributions are deeply valued and appreciated. While all contribution data is available as part of the repository insights, to recognize a significant contribution and hence add the contributor to the package authors list, the following rules are enforced:

    - +

    *Excluding auto-generated code, including but not limited to roxygen comments or renv.lock files.

    The package maintainer also reserves the right to adjust the criteria to recognize contributions.

    -

    Questions

    +

    Questions +

    If you have further questions regarding the contribution guidelines, please contact the package/repository maintainer.

    + + + + - - + + diff --git a/LICENSE-text.html b/LICENSE-text.html index 4511752a..7b0db3dc 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -1,8 +1,22 @@ - -License • teal.modules.hermes + + + + + + + Skip to contents @@ -18,32 +32,38 @@ + - + + - + @@ -69,17 +89,19 @@ limitations under the License. - + + + + - - + + diff --git a/SECURITY.html b/SECURITY.html index 7d69506b..c22fa831 100644 --- a/SECURITY.html +++ b/SECURITY.html @@ -1,8 +1,22 @@ - -Security Policy • teal.modules.hermes + + + + + + + Skip to contents @@ -18,32 +32,38 @@ + - + + - + @@ -57,38 +77,44 @@
    -

    Reporting Security Issues

    +

    Reporting Security Issues +

    If you believe you have found a security vulnerability in any of the repositories in this organization, please report it to us through coordinated disclosure.

    Please do not report security vulnerabilities through public GitHub issues, discussions, or pull requests.

    Instead, please send an email to vulnerability.management[@]roche.com.

    Please include as much of the information listed below as you can to help us better understand and resolve the issue:

    -
    • The type of issue (e.g., buffer overflow, SQL injection, or cross-site scripting)
      • +
        +
      • The type of issue (e.g., buffer overflow, SQL injection, or cross-site scripting)
      • Full paths of source file(s) related to the manifestation of the issue
      • The location of the affected source code (tag/branch/commit or direct URL)
      • Any special configuration required to reproduce the issue
      • Step-by-step instructions to reproduce the issue
      • Proof-of-concept or exploit code (if possible)
      • Impact of the issue, including how an attacker might exploit the issue
        • -

      This information will help us triage your report more quickly.

      +
    +

    This information will help us triage your report more quickly.

    -

    Data Security Standards (DSS)

    +

    Data Security Standards (DSS) +

    Please make sure that while reporting issues in the form a bug, feature, or pull request, all sensitive information such as PII, PHI, and PCI is completely removed from any text and attachments, including pictures and videos.

    + + + + - - + + diff --git a/authors.html b/authors.html index 80411635..39ee468e 100644 --- a/authors.html +++ b/authors.html @@ -1,8 +1,22 @@ - -Authors and Citation • teal.modules.hermes + + + + + + + Skip to contents @@ -18,32 +32,38 @@ + - + + - + @@ -56,7 +76,8 @@

    Authors

    -
    + +

    Citation

    @@ -139,17 +161,19 @@

    Citation

    }
    + + + + - - + + diff --git a/latest-tag/404.html b/latest-tag/404.html index 121d7de9..69162f4e 100644 --- a/latest-tag/404.html +++ b/latest-tag/404.html @@ -1,5 +1,4 @@ - - + @@ -44,14 +43,15 @@ Changelog
  • -
    main + +
    + main latest-tag v0.1.6 v0.1.5 -v0.1.4
    • +v0.1.4 + + + + - + @@ -60,65 +80,80 @@
    -

    Our Pledge

    +

    Our Pledge +

    We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.

    We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.

    -

    Our Standards

    +

    Our Standards +

    Examples of behavior that contributes to a positive environment for our community include:

    -
    • Demonstrating empathy and kindness toward other people
      • +
        +
      • Demonstrating empathy and kindness toward other people
      • Being respectful of differing opinions, viewpoints, and experiences
      • Giving and gracefully accepting constructive feedback
      • Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
      • Focusing on what is best not just for us as individuals, but for the overall community
        • -

      Examples of unacceptable behavior include:

      -
      • The use of sexualized language or imagery, and sexual attention or advances of any kind
        • +
      +

      Examples of unacceptable behavior include:

      +
        +
      • The use of sexualized language or imagery, and sexual attention or advances of any kind
      • Trolling, insulting or derogatory comments, and personal or political attacks
      • Public or private harassment
      • Publishing others’ private information, such as a physical or email address, without their explicit permission
      • Other conduct which could reasonably be considered inappropriate in a professional setting
        • -
    + +
    -

    Enforcement Responsibilities

    +

    Enforcement Responsibilities +

    Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.

    Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.

    -

    Scope

    +

    Scope +

    This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.

    -

    Enforcement

    +

    Enforcement +

    Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at [INSERT CONTACT METHOD]. All complaints will be reviewed and investigated promptly and fairly.

    All community leaders are obligated to respect the privacy and security of the reporter of any incident.

    -

    Enforcement Guidelines

    +

    Enforcement Guidelines +

    Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:

    -

    1. Correction

    +

    1. Correction +

    Community Impact: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.

    Consequence: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.

    -

    2. Warning

    +

    2. Warning +

    Community Impact: A violation through a single incident or series of actions.

    Consequence: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.

    -

    3. Temporary Ban

    +

    3. Temporary Ban +

    Community Impact: A serious violation of community standards, including sustained inappropriate behavior.

    Consequence: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.

    -

    4. Permanent Ban

    +

    4. Permanent Ban +

    Community Impact: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.

    Consequence: A permanent ban from any sort of public interaction within the community.

    -

    Attribution

    +

    Attribution +

    This Code of Conduct is adapted from the Contributor Covenant, version 2.1, available at https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.

    Community Impact Guidelines were inspired by Mozilla’s code of conduct enforcement ladder.

    For answers to common questions about this code of conduct, see the FAQ at https://www.contributor-covenant.org/faq. Translations are available at https://www.contributor-covenant.org/translations.

    @@ -126,17 +161,19 @@

    Attribution

    + + + + - - + + diff --git a/latest-tag/CONTRIBUTING.html b/latest-tag/CONTRIBUTING.html index 8bbe79a3..2a20c6b3 100644 --- a/latest-tag/CONTRIBUTING.html +++ b/latest-tag/CONTRIBUTING.html @@ -1,8 +1,22 @@ - -Contribution Guidelines • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + - + @@ -62,7 +82,8 @@

    🙏 Thank you for taking the time to contribute!

    Your input is deeply valued, whether an issue, a pull request, or even feedback, regardless of size, content or scope.

    -

    Table of contents

    +

    Table of contents +

    👶 Getting started

    📔 Code of Conduct

    🗃 License

    @@ -73,38 +94,47 @@

    Table of contents❓ Questions

    -

    Getting started

    +

    Getting started +

    Please refer the project documentation for a brief introduction. Please also see other articles within the project documentation for additional information.

    -

    Code of Conduct

    +

    Code of Conduct +

    A Code of Conduct governs this project. Participants and contributors are expected to follow the rules outlined therein.

    -

    License

    +

    License +

    All your contributions will be covered by this project’s license.

    -

    Issues

    +

    Issues +

    We use GitHub to track issues, feature requests, and bugs. Before submitting a new issue, please check if the issue has already been reported. If the issue already exists, please upvote the existing issue 👍.

    For new feature requests, please elaborate on the context and the benefit the feature will have for users, developers, or other relevant personas.

    -

    Pull requests

    +

    Pull requests +

    -

    GitHub Flow

    +

    GitHub Flow +

    This repository uses the GitHub Flow model for collaboration. To submit a pull request:

    -
    1. +
        +

      1. Create a branch

        Please see the branch naming convention below. If you don’t have write access to this repository, please fork it.

      2. Make changes

        Make sure your code

        -
        • passes all checks imposed by GitHub Actions
          • +
            +
          • passes all checks imposed by GitHub Actions
          • is well documented
          • is well tested with unit tests sufficiently covering the changes introduced
            • -
          +
        +

      3. Create a pull request (PR)

        In the pull request description, please link the relevant issue (if any), provide a detailed description of the change, and include any assumptions.

        @@ -118,76 +148,93 @@

        GitHub Flow -

        Branch naming convention

        +

        Branch naming convention +

        Suppose your changes are related to a current issue in the current project; please name your branch as follows: <issue_id>_<short_description>. Please use underscore (_) as a delimiter for word separation. For example, 420_fix_ui_bug would be a suitable branch name if your change is resolving and UI-related bug reported in issue number 420 in the current project.

        If your change affects multiple repositories, please name your branches as follows: <issue_id>_<issue_repo>_<short description>. For example, 69_awesomeproject_fix_spelling_error would reference issue 69 reported in project awesomeproject and aims to resolve one or more spelling errors in multiple (likely related) repositories.

    monorepo and staged.dependencies -

    + +

    Sometimes you might need to change upstream dependent package(s) to be able to submit a meaningful change. We are using staged.dependencies functionality to simulate a monorepo behavior. The dependency configuration is already specified in this project’s staged_dependencies.yaml file. You need to name the feature branches appropriately. This is the only exception from the branch naming convention described above.

    Please refer to the staged.dependencies package documentation for more details.

    -

    Coding guidelines

    +

    Coding guidelines +

    This repository follows some unified processes and standards adopted by its maintainers to ensure software development is carried out consistently within teams and cohesively across other repositories.

    -

    Style guide

    +

    Style guide +

    This repository follows the standard tidyverse style guide and uses lintr for lint checks. Customized lint configurations are available in this repository’s .lintr file.

    -

    Dependency management

    +

    Dependency management +

    Lightweight is the right weight. This repository follows tinyverse recommedations of limiting dependencies to minimum.

    -

    Dependency version management

    +

    Dependency version management +

    If the code is not compatible with all (!) historical versions of a given dependenct package, it is required to specify minimal version in the DESCRIPTION file. In particular: if the development version requires (imports) the development version of another package - it is required to put abc (>= 1.2.3.9000).

    -

    Recommended development environment & tools

    +

    Recommended development environment & tools +

    -

    R & package versions

    +

    R & package versions +

    We continuously test our packages against the newest R version along with the most recent dependencies from CRAN and BioConductor. We recommend that your working environment is also set up in the same way. You can find the details about the R version and packages used in the R CMD check GitHub Action execution log - there is a step that prints out the R sessionInfo().

    If you discover bugs on older R versions or with an older set of dependencies, please create the relevant bug reports.

    -

    pre-commit

    +

    +pre-commit +

    We highly recommend that you use the pre-commit tool combined with R hooks for pre-commit to execute some of the checks before committing and pushing your changes.

    Pre-commit hooks are already available in this repository’s .pre-commit-config.yaml file.

    -

    Recognition model

    +

    Recognition model +

    As mentioned previously, all contributions are deeply valued and appreciated. While all contribution data is available as part of the repository insights, to recognize a significant contribution and hence add the contributor to the package authors list, the following rules are enforced:

    - +

    *Excluding auto-generated code, including but not limited to roxygen comments or renv.lock files.

    The package maintainer also reserves the right to adjust the criteria to recognize contributions.

    -

    Questions

    +

    Questions +

    If you have further questions regarding the contribution guidelines, please contact the package/repository maintainer.

    + + + + - - + + diff --git a/latest-tag/LICENSE-text.html b/latest-tag/LICENSE-text.html index b423548f..85e691d9 100644 --- a/latest-tag/LICENSE-text.html +++ b/latest-tag/LICENSE-text.html @@ -1,8 +1,22 @@ - -License • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + - + @@ -72,17 +92,19 @@ limitations under the License. - + + + + - - + + diff --git a/latest-tag/SECURITY.html b/latest-tag/SECURITY.html index 8ca9c588..c6da2650 100644 --- a/latest-tag/SECURITY.html +++ b/latest-tag/SECURITY.html @@ -1,8 +1,22 @@ - -Security Policy • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + - + @@ -60,38 +80,44 @@
    -

    Reporting Security Issues

    +

    Reporting Security Issues +

    If you believe you have found a security vulnerability in any of the repositories in this organization, please report it to us through coordinated disclosure.

    Please do not report security vulnerabilities through public GitHub issues, discussions, or pull requests.

    Instead, please send an email to vulnerability.management[@]roche.com.

    Please include as much of the information listed below as you can to help us better understand and resolve the issue:

    -
    • The type of issue (e.g., buffer overflow, SQL injection, or cross-site scripting)
      • +
        +
      • The type of issue (e.g., buffer overflow, SQL injection, or cross-site scripting)
      • Full paths of source file(s) related to the manifestation of the issue
      • The location of the affected source code (tag/branch/commit or direct URL)
      • Any special configuration required to reproduce the issue
      • Step-by-step instructions to reproduce the issue
      • Proof-of-concept or exploit code (if possible)
      • Impact of the issue, including how an attacker might exploit the issue
        • -

      This information will help us triage your report more quickly.

      +
    +

    This information will help us triage your report more quickly.

    -

    Data Security Standards (DSS)

    +

    Data Security Standards (DSS) +

    Please make sure that while reporting issues in the form a bug, feature, or pull request, all sensitive information such as PII, PHI, and PCI is completely removed from any text and attachments, including pictures and videos.

    + + + + - - + + diff --git a/latest-tag/articles/Getting_Started.html b/latest-tag/articles/Getting_Started.html index 2a32b1ea..7a27498e 100644 --- a/latest-tag/articles/Getting_Started.html +++ b/latest-tag/articles/Getting_Started.html @@ -1,5 +1,4 @@ - - + @@ -46,14 +45,15 @@ Changelog
  • -
    main + +
    + main latest-tag v0.1.6 v0.1.5 -v0.1.4
    • +v0.1.4 + + + + - + @@ -60,20 +80,25 @@

    All vignettes

    -
    Getting Started
    +
    +
    Getting Started
    -
    - + +
    + + + + + - - + + diff --git a/latest-tag/authors.html b/latest-tag/authors.html index 88333e84..4564cea7 100644 --- a/latest-tag/authors.html +++ b/latest-tag/authors.html @@ -1,8 +1,22 @@ - -Authors and Citation • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + - + @@ -59,7 +79,8 @@

    Authors

    -
    + +

    Citation

    @@ -148,17 +170,19 @@

    Citation

    }
    + + + + - - + + diff --git a/latest-tag/index.html b/latest-tag/index.html index 396804f3..4ab25fcd 100644 --- a/latest-tag/index.html +++ b/latest-tag/index.html @@ -1,5 +1,4 @@ - - + @@ -46,14 +45,15 @@ Changelog
  • -
    main + +
    + main latest-tag v0.1.6 v0.1.5 -v0.1.4
    • +v0.1.4 + + + + - + @@ -58,78 +78,119 @@
    -

    teal.modules.hermes 0.1.6

    +

    teal.modules.hermes 0.1.6 +

    -

    Miscellaneous

    -
    • Added placeholders for assaySpec, adtteSpec and geneSpec inputs when no option is selected.
      • +

      Miscellaneous +

      +
        +
      • Added placeholders for assaySpec, adtteSpec and geneSpec inputs when no option is selected.
      • Disabled the select input for assaySpec and adtteSpec when there are no options available.
      • For module developers: The module gets teal_data object in the UI and reactive(<teal_data>) in the server
        • -
    + +
    -

    Enhancements

    -
    +

    Enhancements +

    + +
    -

    teal.modules.hermes 0.1.5

    +

    teal.modules.hermes 0.1.5 +

    -

    Bug Fixes

    -
    • Filtering data with the filter panel now correctly triggers the sampleVarSpecModule.
      • -
    +

    Bug Fixes +

    + +
    -

    Breaking changes

    -
    +

    Breaking changes +

    + +
    -

    Miscellaneous

    -
    + +
    -

    teal.modules.hermes 0.1.4

    -
    + +
    -

    teal.modules.hermes 0.1.3

    -
    -

    Miscellaneous

    -
    • Added a template to the pkgdown site.
      • +

      teal.modules.hermes 0.1.3 +

      +
        +
      • Improve the selection of sample variables in the forest module (tm_g_forest_tte) such that only categorical variables can be selected in the first place.
        • +
      +
      +

      Miscellaneous +

      +
        +
      • Added a template to the pkgdown site.
      • Updated package authors.
      • Added the option categorical_only to the sampleVarSpec server module, which allows to only show categorical sample variables for selection.
        • -
      +
    +
    -

    teal.modules.hermes 0.1.2

    -
    + +
    -

    teal.modules.hermes 0.1.1

    +

    teal.modules.hermes 0.1.1 +

    -

    Bug Fixes

    -
    • Updated legend for the PCA plot.
      • +

      Bug Fixes +

      +
        +
      • Updated legend for the PCA plot.
      • Gene selection with more than a few thousand genes no longer hangs the application. This is achieved through a different selection input in the corresponding geneSpec shiny module.
      • Only atomic columns of colData with at least one value can now be selected in the sampleVarSpecModule.
        • -
    + +
    -

    Miscellaneous

    -
    + +
    -

    teal.modules.hermes 0.1.0

    - +
    + + + + - - + + diff --git a/latest-tag/pull_request_template.html b/latest-tag/pull_request_template.html index 576c50ff..8da717e2 100644 --- a/latest-tag/pull_request_template.html +++ b/latest-tag/pull_request_template.html @@ -1,8 +1,22 @@ - -Pull Request • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + - + @@ -63,17 +83,19 @@

    Fixes #nnn

    - + + + + - - + + diff --git a/latest-tag/reference/adtteSpecInput.html b/latest-tag/reference/adtteSpecInput.html index 878d6d91..43f5b3ae 100644 --- a/latest-tag/reference/adtteSpecInput.html +++ b/latest-tag/reference/adtteSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for ADTTE Specification — adtteSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + - + @@ -66,13 +88,16 @@
    -

    Usage

    +

    Usage +

    adtteSpecInput(inputId, label_paramcd = "Select Endpoint")
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -80,30 +105,35 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    adtteSpecServer() for the module server and a complete example.

    + + + + - - + + diff --git a/latest-tag/reference/adtteSpecServer.html b/latest-tag/reference/adtteSpecServer.html index 868a9931..3457966c 100644 --- a/latest-tag/reference/adtteSpecServer.html +++ b/latest-tag/reference/adtteSpecServer.html @@ -1,18 +1,34 @@ - - + + + + + +Module Server for ADTTE Specification — adtteSpecServer • teal.modules.hermes +Module Server for ADTTE Specification — adtteSpecServer • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -28,7 +44,8 @@ + - + + - + @@ -78,7 +100,8 @@
    -

    Usage

    +

    Usage +

    adtteSpecServer(
   id,
   data,
@@ -94,8 +117,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -115,8 +140,11 @@

    ArgumentsArgumentsArguments -

    Value

    +

    Value +

    -

    List with the following elements:

    • binned_adtte_subset: reactive containing the joined ADTTE and gene data.

      • +

      List with the following elements:

      +
        +

      • binned_adtte_subset: reactive containing the joined ADTTE and gene data.

      • gene_col: reactive containing the string with the column name of the original numeric gene variable.

      • gene_factor: string with the variable name for the binned gene data.

      • time_unit: reactive string with the time unit for the current subset.

        • -
    + +
    -

    See also

    +

    See also +

    adtteSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id) {
   ns <- NS(id)
 
@@ -260,17 +296,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/assaySpecInput.html b/latest-tag/reference/assaySpecInput.html index 1d70983e..4369a34a 100644 --- a/latest-tag/reference/assaySpecInput.html +++ b/latest-tag/reference/assaySpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Assay Specification — assaySpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,13 +88,16 @@
    -

    Usage

    +

    Usage +

    assaySpecInput(inputId, label_assays = "Select Assay")
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -80,30 +105,35 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    assaySpecServer() for the module server and a complete example.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/latest-tag/reference/assaySpecServer.html b/latest-tag/reference/assaySpecServer.html index 2f148680..8e1f92ca 100644 --- a/latest-tag/reference/assaySpecServer.html +++ b/latest-tag/reference/assaySpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Assay Specification — assaySpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,13 +88,16 @@
    -

    Usage

    +

    Usage +

    assaySpecServer(id, assays, exclude_assays = character())
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -84,20 +109,24 @@

    Arguments -

    Value

    +

    Value +

    The chosen assay as a reactive string.

    -

    See also

    +

    See also +

    assaySpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id) {
   ns <- NS(id)
   teal.widgets::standard_layout(
@@ -155,17 +184,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/assert_adtte_vars.html b/latest-tag/reference/assert_adtte_vars.html index 1860e3f8..64afbbb7 100644 --- a/latest-tag/reference/assert_adtte_vars.html +++ b/latest-tag/reference/assert_adtte_vars.html @@ -1,10 +1,26 @@ - -Check for ADTTE Variables — assert_adtte_vars • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,38 +88,46 @@
    -

    Usage

    +

    Usage +

    assert_adtte_vars(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    -
    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    assert_adtte_vars(list(aval = "AV", is_event = "EV", paramcd = "PC", usubjid = "ID", avalu = "u"))
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/latest-tag/reference/assert_summary_funs.html b/latest-tag/reference/assert_summary_funs.html index 859aa865..30570fe5 100644 --- a/latest-tag/reference/assert_summary_funs.html +++ b/latest-tag/reference/assert_summary_funs.html @@ -1,10 +1,26 @@ - -Check for List of Summary Functions — assert_summary_funs • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,13 +88,16 @@
    -

    Usage

    +

    Usage +

    assert_summary_funs(x, null.ok = FALSE)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    @@ -80,29 +105,34 @@

    Arguments -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    assert_summary_funs(list(mean = colMeans, raw = NULL), null.ok = TRUE)
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/latest-tag/reference/assertion_arguments.html b/latest-tag/reference/assertion_arguments.html index a831d618..ec0081fd 100644 --- a/latest-tag/reference/assertion_arguments.html +++ b/latest-tag/reference/assertion_arguments.html @@ -1,10 +1,26 @@ - -Standard Assertion Arguments — assertion_arguments • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -67,8 +89,10 @@
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    @@ -95,19 +119,22 @@

    Argumentscheckmate::vname().

    -

    + + - + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/latest-tag/reference/assertions.html b/latest-tag/reference/assertions.html index cc5385df..665dc153 100644 --- a/latest-tag/reference/assertions.html +++ b/latest-tag/reference/assertions.html @@ -1,14 +1,30 @@ - - + + + + + +Additional Assertions for checkmate — assertions • teal.modules.hermes +Additional Assertions for checkmate — assertions • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    +
    -

    Additional Assertions for checkmate

    +

    Additional Assertions for checkmate +

    Source: R/checkmate.R
    assertions.Rd
    @@ -73,32 +96,39 @@
    -

    Value

    +

    Value +

    -

    Depending on the function prefix.

    • assert_ functions return the object invisibly if successful, and otherwise +

      Depending on the function prefix.

      +
        +

      • assert_ functions return the object invisibly if successful, and otherwise throw an error message.

      • check_ functions return TRUE if successful, otherwise a string with the error message.

      • test_ functions just return TRUE or FALSE.

        • -
    + +
    -

    See also

    +

    See also +

    assert_tag(), assert_reactive(), assert_summary_funs(), assert_adtte_vars()

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/latest-tag/reference/check_reactive.html b/latest-tag/reference/check_reactive.html index fbb86217..bb9c8783 100644 --- a/latest-tag/reference/check_reactive.html +++ b/latest-tag/reference/check_reactive.html @@ -1,10 +1,26 @@ - -Check for Reactive Input — check_reactive • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    check_reactive(x)
 
 assert_reactive(x, .var.name = checkmate::vname(x), add = NULL)
@@ -75,8 +98,10 @@ 
    Usage
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    @@ -89,14 +114,17 @@

    Argumentscheckmate::AssertCollection.

    -

    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    check_reactive("bla")
 #> [1] FALSE
 check_reactive(reactive("bla"))
@@ -104,17 +132,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/check_tag.html b/latest-tag/reference/check_tag.html index a1facee1..9e42b418 100644 --- a/latest-tag/reference/check_tag.html +++ b/latest-tag/reference/check_tag.html @@ -1,10 +1,26 @@ - -Check for Shiny Tag — check_tag • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    check_tag(x, null.ok = FALSE)
 
 assert_tag(x, null.ok = FALSE, .var.name = checkmate::vname(x), add = NULL)
@@ -77,8 +100,10 @@ 
    Usage
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    @@ -105,14 +130,17 @@

    Argumentscheckmate::vname().

    -

    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    check_tag("bla")
 #> [1] "Must be a 'shiny.tag' or NULL"
 check_tag(NULL, null.ok = TRUE)
@@ -120,17 +148,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/experimentSpecInput.html b/latest-tag/reference/experimentSpecInput.html index f26a31ed..9ed6808e 100644 --- a/latest-tag/reference/experimentSpecInput.html +++ b/latest-tag/reference/experimentSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Experiment Specification — experimentSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    experimentSpecInput(
   inputId,
   data,
@@ -76,8 +99,10 @@ 
    Usage
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -95,30 +120,35 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    experimentSpecServer() for the module server and a complete example.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/latest-tag/reference/experimentSpecServer.html b/latest-tag/reference/experimentSpecServer.html index 4e7f4fc1..a4ea71b2 100644 --- a/latest-tag/reference/experimentSpecServer.html +++ b/latest-tag/reference/experimentSpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Experiment Specification — experimentSpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    experimentSpecServer(
   id,
   data,
@@ -79,8 +102,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -113,23 +138,30 @@

    Arguments -

    Value

    +

    Value +

    -

    List with the following reactive objects:

    • data: the hermes::AnyHermesData experiment.

      • +

      List with the following reactive objects:

      +
        +

      • data: the hermes::AnyHermesData experiment.

      • name: the name of the experiment as selected by the user.

      • genes: a data.frame with the genes in data, with columns id and name.

      • assays: the names of the assays in data.

        • -
    + +
    -

    See also

    +

    See also +

    experimentSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                mae_name) {
   ns <- NS(id)
@@ -211,17 +243,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/function_arguments.html b/latest-tag/reference/function_arguments.html index 7532e036..ddbb5ef5 100644 --- a/latest-tag/reference/function_arguments.html +++ b/latest-tag/reference/function_arguments.html @@ -1,10 +1,26 @@ - -Standard Function Arguments — function_arguments • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -67,8 +89,10 @@
    -

    Arguments

    -
    adtte
    +

    Arguments +

    +
    +
    adtte

    (data frame)
    an adtte dataset.

    @@ -96,19 +120,22 @@

    Arguments

    teal.modules.hermes is a part of the NEST and pharmaverse.

    - + + - - + + diff --git a/latest-tag/reference/geneSpecInput.html b/latest-tag/reference/geneSpecInput.html index b4762ece..d6a48b9b 100644 --- a/latest-tag/reference/geneSpecInput.html +++ b/latest-tag/reference/geneSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Gene Signature Specification — geneSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    geneSpecInput(
   inputId,
   funs,
@@ -83,8 +106,10 @@ 
    Usage
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -126,20 +151,24 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    geneSpecServer() for the module server and a complete example.

    -

    Examples

    +

    Examples +

    geneSpecInput("my_genes", list(mean = colMeans), label_funs = "Please select function")
 #> <div class="row">
 #>   <div class="col-sm-8">
@@ -205,17 +234,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/geneSpecServer.html b/latest-tag/reference/geneSpecServer.html index df102e7f..ca698ce9 100644 --- a/latest-tag/reference/geneSpecServer.html +++ b/latest-tag/reference/geneSpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Gene Signature Specification — geneSpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    geneSpecServer(
   id,
   funs,
@@ -78,8 +101,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -100,21 +125,25 @@

    Arguments -

    Value

    +

    Value +

    Reactive hermes::GeneSpec which can be used as input for the relevant hermes functions.

    -

    See also

    +

    See also +

    geneSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id, funs) {
   ns <- NS(id)
   teal.widgets::standard_layout(
@@ -184,17 +213,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/h_assign_to_group_list.html b/latest-tag/reference/h_assign_to_group_list.html index 9063676f..99370c98 100644 --- a/latest-tag/reference/h_assign_to_group_list.html +++ b/latest-tag/reference/h_assign_to_group_list.html @@ -1,12 +1,28 @@ - - + + + + + +Helper Function For Group List Creation — h_assign_to_group_list • teal.modules.hermes +Helper Function For Group List Creation — h_assign_to_group_list • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,25 +91,31 @@
    -

    Usage

    +

    Usage +

    h_assign_to_group_list(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (named list of character)
    input assignment list.

    -
    + +
    -

    Value

    +

    Value +

    A combination list.

    -

    Examples

    +

    Examples +

    assign_list <- list(
   "ASIAN" = "1",
   "BLACK OR AFRICAN AMERICAN" = "1",
@@ -105,17 +133,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/h_collapse_levels.html b/latest-tag/reference/h_collapse_levels.html index ebb61723..17a85628 100644 --- a/latest-tag/reference/h_collapse_levels.html +++ b/latest-tag/reference/h_collapse_levels.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function for Collapsing of Factor Levels — h_collapse_levels • teal.modules.hermes +Helper Function for Collapsing of Factor Levels — h_collapse_levels • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,13 +94,16 @@
    -

    Usage

    +

    Usage +

    h_collapse_levels(x, group_list)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (factor)
    original factor.

    @@ -86,16 +111,19 @@

    Arguments -

    Value

    +

    Value +

    The transformed factor x with new levels.

    -

    Examples

    +

    Examples +

    set.seed(123)
 x <- factor(sample(
   c("ASIAN", "BLACK OR AFRICAN AMERICAN", "MULTIPLE", "UNKNOWN", "WHITE"),
@@ -112,17 +140,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/h_extract_words.html b/latest-tag/reference/h_extract_words.html index af36d3f9..49c91294 100644 --- a/latest-tag/reference/h_extract_words.html +++ b/latest-tag/reference/h_extract_words.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Extract Words — h_extract_words • teal.modules.hermes +Helper Function to Extract Words — h_extract_words • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,25 +94,31 @@
    -

    Usage

    +

    Usage +

    h_extract_words(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (string)
    input.

    -
    + +
    -

    Value

    +

    Value +

    Character vector with the extracted words.

    -

    Examples

    +

    Examples +

    h_extract_words("a, b, , c, 234; 34562 - GeneID:bla")
 #> [1] "a"          "b"          "c"          "234"        "34562"     
 #> [6] "GeneID:bla"
@@ -99,17 +127,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/h_gene_data.html b/latest-tag/reference/h_gene_data.html index 3e91f4b8..cb85deb2 100644 --- a/latest-tag/reference/h_gene_data.html +++ b/latest-tag/reference/h_gene_data.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Format Gene Choices — h_gene_data • teal.modules.hermes +Helper Function to Format Gene Choices — h_gene_data • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,13 +94,16 @@
    -

    Usage

    +

    Usage +

    h_gene_data(object, name_annotation)
    -

    Arguments

    -
    object
    +

    Arguments +

    +
    +
    object

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    @@ -87,23 +112,27 @@

    Arguments -

    Value

    +

    Value +

    A data.frame with id and name columns containing all genes from object.

    -

    Details

    +

    Details +

    Note that missing names or names that only contain whitespace are replaced by empty strings for consistency and better labeling in the UI downstream

    -

    Examples

    +

    Examples +

    object <- hermes::hermes_data[1:10, ]
 h_gene_data(object, "symbol")
 #>                  id         name
@@ -120,17 +149,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/h_km_mae_to_adtte.html b/latest-tag/reference/h_km_mae_to_adtte.html index c1154486..fefb036a 100644 --- a/latest-tag/reference/h_km_mae_to_adtte.html +++ b/latest-tag/reference/h_km_mae_to_adtte.html @@ -1,10 +1,26 @@ - -Data Preprocessing for ADTTE Module — h_km_mae_to_adtte • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    h_km_mae_to_adtte(
   adtte,
   mae,
@@ -78,8 +101,10 @@ 
    Usage
    -

    Arguments

    -
    adtte
    +

    Arguments +

    +
    +
    adtte

    (data frame)
    an adtte dataset.

    @@ -103,9 +128,11 @@

    Arguments -

    Value

    +

    Value +

    A data frame containing all columns/rows from adtte that match @@ -114,13 +141,15 @@

    Value

    -

    Note

    +

    Note +

    The final gene column names can start with a different string than the original gene IDs (or labels), in particular white space and colons are removed.

    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 adtte <- teal.modules.hermes::rADTTE %>%
   dplyr::mutate(CNSR = as.logical(CNSR))
@@ -146,17 +175,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/h_order_genes.html b/latest-tag/reference/h_order_genes.html index f70fccd2..20eab4de 100644 --- a/latest-tag/reference/h_order_genes.html +++ b/latest-tag/reference/h_order_genes.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Order Gene Choices — h_order_genes • teal.modules.hermes +Helper Function to Order Gene Choices — h_order_genes • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,26 +94,32 @@
    -

    Usage

    +

    Usage +

    h_order_genes(genes)
    -

    Arguments

    -
    genes
    +

    Arguments +

    +
    +
    genes

    (data.frame)
    containing id and name columns of the gene choices. Note that no missing values are allowed.

    -
    + +
    -

    Value

    +

    Value +

    The ordered data.frame.

    -

    Examples

    +

    Examples +

    genes <- data.frame(
   id = c("7", "1", "2", "345346", "0"),
   name = c("e", "", "c", "", "a")
@@ -106,17 +134,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/h_parse_genes.html b/latest-tag/reference/h_parse_genes.html index eb7c7b8a..6acab47a 100644 --- a/latest-tag/reference/h_parse_genes.html +++ b/latest-tag/reference/h_parse_genes.html @@ -1,12 +1,28 @@ - - + + + + + +Helper Function to Parse Genes — h_parse_genes • teal.modules.hermes +Helper Function to Parse Genes — h_parse_genes • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,13 +91,16 @@
    -

    Usage

    +

    Usage +

    h_parse_genes(words, choices)
    -

    Arguments

    -
    words
    +

    Arguments +

    +
    +
    words

    (character)
    containing gene IDs or names.

    @@ -83,16 +108,19 @@

    Arguments -

    Value

    +

    Value +

    The subset of choices which matches words in ID or name.

    -

    Examples

    +

    Examples +

    h_parse_genes(
   c("a", "2535"),
   data.frame(id = as.character(2533:2537), name = letters[1:5])
@@ -103,17 +131,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/h_update_gene_selection.html b/latest-tag/reference/h_update_gene_selection.html index 2222c383..9232dc67 100644 --- a/latest-tag/reference/h_update_gene_selection.html +++ b/latest-tag/reference/h_update_gene_selection.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Update Gene Selection — h_update_gene_selection • teal.modules.hermes +Helper Function to Update Gene Selection — h_update_gene_selection • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,13 +94,16 @@
    -

    Usage

    +

    Usage +

    h_update_gene_selection(session, inputId, selected, choices)
    -

    Arguments

    -
    session
    +

    Arguments +

    +
    +
    session

    (ShinySession)
    the session object.

    @@ -95,20 +120,23 @@

    Arguments

    + + + + - - + + diff --git a/latest-tag/reference/heatmap_plot.html b/latest-tag/reference/heatmap_plot.html index 89300972..2ab14d2c 100644 --- a/latest-tag/reference/heatmap_plot.html +++ b/latest-tag/reference/heatmap_plot.html @@ -1,10 +1,26 @@ - -Correlation Heatmap Plot — heatmap_plot • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,29 +88,35 @@
    -

    Usage

    +

    Usage +

    heatmap_plot(object, assay_name)
    -

    Arguments

    -
    object
    +

    Arguments +

    +
    +
    object

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    assay_name

    (string)
    the assay to define the groups.

    -
    + +
    -

    Value

    +

    Value +

    Plot to be displayed in the teal app.

    -

    Examples

    +

    Examples +

    library(hermes)
 #> Loading required package: ggfortify
 #> Loading required package: SummarizedExperiment
@@ -164,17 +192,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/include_css_files.html b/latest-tag/reference/include_css_files.html index c28212b2..5546230c 100644 --- a/latest-tag/reference/include_css_files.html +++ b/latest-tag/reference/include_css_files.html @@ -1,12 +1,28 @@ - - + + + + + +Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.modules.hermes +Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,35 +91,42 @@
    -

    Usage

    +

    Usage +

    include_css_files(pattern = "*")
    -

    Arguments

    -
    pattern
    +

    Arguments +

    +
    +
    pattern

    (character) pattern of files to be included

    -
    + +
    -

    Value

    +

    Value +

    HTML code that includes CSS files

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/latest-tag/reference/include_js_files.html b/latest-tag/reference/include_js_files.html index 9b8268d6..5b5e3d4d 100644 --- a/latest-tag/reference/include_js_files.html +++ b/latest-tag/reference/include_js_files.html @@ -1,12 +1,28 @@ - - + + + + + +Include JS files from /inst/js/ package directory to application header — include_js_files • teal.modules.hermes +Include JS files from /inst/js/ package directory to application header — include_js_files • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,39 +91,46 @@
    -

    Usage

    +

    Usage +

    include_js_files(pattern = "*")
    -

    Arguments

    -
    pattern
    +

    Arguments +

    +
    +
    pattern

    (character) pattern of files to be included, passed to system.file

    except

    (character) vector of basename filenames to be excluded

    -
    + +
    -

    Value

    +

    Value +

    HTML code that includes JS files

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/latest-tag/reference/index.html b/latest-tag/reference/index.html index 48989a39..f75b5cbc 100644 --- a/latest-tag/reference/index.html +++ b/latest-tag/reference/index.html @@ -1,8 +1,22 @@ - -Function reference • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -57,280 +77,377 @@
    -

    Package

    +

    Package +

    -
    +
    +
    -
    +
    +
    teal.modules.hermes teal.modules.hermes-package
    -
    teal.modules.hermes Package
    -
    -

    Utility Functions

    +
    +teal.modules.hermes Package
    + +
    +
    +

    Utility Functions +

    -
    +
    +
    -
    +
    +
    h_assign_to_group_list()
    Helper Function For Group List Creation
    -
    +
    +
    +
    h_collapse_levels()
    Helper Function for Collapsing of Factor Levels
    -
    +
    +
    +
    h_extract_words()
    Helper Function to Extract Words
    -
    +
    +
    +
    h_gene_data()
    Helper Function to Format Gene Choices
    -
    +
    +
    +
    h_km_mae_to_adtte()
    Data Preprocessing for ADTTE Module
    -
    +
    +
    +
    h_order_genes()
    Helper Function to Order Gene Choices
    -
    +
    +
    +
    h_parse_genes()
    Helper Function to Parse Genes
    -
    +
    +
    +
    h_update_gene_selection()
    Helper Function to Update Gene Selection
    -
    +
    +
    +
    is_blank()
    Checking for Empty String
    -
    -

    Shiny Modules

    + +
    +
    +

    Shiny Modules +

    -
    +
    +
    -
    +
    +
    adtteSpecInput()
    Module Input for ADTTE Specification
    -
    +
    +
    +
    adtteSpecServer()
    Module Server for ADTTE Specification
    -
    +
    +
    +
    assaySpecInput()
    Module Input for Assay Specification
    -
    +
    +
    +
    assaySpecServer()
    Module Server for Assay Specification
    -
    +
    +
    +
    experimentSpecInput()
    Module Input for Experiment Specification
    -
    +
    +
    +
    experimentSpecServer()
    Module Server for Experiment Specification
    -
    +
    +
    +
    geneSpecInput()
    Module Input for Gene Signature Specification
    -
    +
    +
    +
    geneSpecServer()
    Module Server for Gene Signature Specification
    -
    +
    +
    +
    sampleVarSpecInput()
    Module Input for Sample Variable Specification
    -
    +
    +
    +
    sampleVarSpecServer()
    Module Server for Sample Variable Specification
    -
    +
    +
    +
    multiSampleVarSpecServer()
    Module Server for Specification of Multiple Sample Variables
    -
    -

    Teal Module Functions

    + +
    +
    +

    Teal Module Functions +

    -
    +
    +
    -
    +
    +
    tm_g_barplot() ui_g_barplot() srv_g_barplot() sample_tm_g_barplot()
    Teal Module for RNA-seq Barplot
    -
    +
    +
    +
    tm_g_boxplot() ui_g_boxplot() srv_g_boxplot() sample_tm_g_boxplot()
    Teal Module for RNA-seq Boxplot
    -
    +
    +
    +
    tm_g_forest_tte() ui_g_forest_tte() srv_g_forest_tte() sample_tm_g_forest_tte()
    Teal Module for Survival Forest Plot
    -
    +
    +
    +
    tm_g_km() ui_g_km() srv_g_km() sample_tm_g_km()
    Teal Module for Kaplan-Meier Plot
    -
    +
    +
    +
    tm_g_pca() ui_g_pca() srv_g_pca() sample_tm_g_pca()
    Teal Module for PCA Analysis
    -
    +
    +
    +
    tm_g_quality() ui_g_quality() srv_g_quality() sample_tm_g_quality()
    Teal Module for RNA-seq Quality Control
    -
    +
    +
    +
    tm_g_scatterplot() ui_g_scatterplot() srv_g_scatterplot() sample_tm_g_scatterplot()
    Teal Module for RNA-seq Scatterplot
    -
    +
    +
    +
    tm_g_volcanoplot() ui_g_volcanoplot() srv_g_volcanoplot() sample_tm_g_volcanoplot()
    Teal Module for RNA-seq Volcano Plot
    -
    -

    Graph Functions

    + +
    +
    +

    Graph Functions +

    -
    +
    +
    -
    +
    +
    heatmap_plot()
    Correlation Heatmap Plot
    -
    +
    +
    +
    top_gene_plot()
    Most Expressed Genes Plot
    -
    -

    Assertions

    + +
    +
    +

    Assertions +

    -
    +
    +
    -
    +
    +
    assert_adtte_vars()
    Check for ADTTE Variables
    -
    +
    +
    +
    check_reactive() assert_reactive() test_reactive()
    Check for Reactive Input
    -
    +
    +
    +
    assert_summary_funs()
    Check for List of Summary Functions
    -
    +
    +
    +
    check_tag() assert_tag() test_tag() expect_tag()
    Check for Shiny Tag
    -
    -

    Validations

    + +
    +
    +

    Validations +

    -
    +
    +
    -
    +
    +
    validate_gene_spec()
    Validation of Gene Specification
    -
    +
    +
    +
    validate_n_levels()
    Validation of Number of Levels
    -
    + + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/latest-tag/reference/is_blank.html b/latest-tag/reference/is_blank.html index 504fdbd9..0218ae9e 100644 --- a/latest-tag/reference/is_blank.html +++ b/latest-tag/reference/is_blank.html @@ -1,12 +1,28 @@ - - + + + + + +Checking for Empty String — is_blank • teal.modules.hermes +Checking for Empty String — is_blank • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,25 +91,31 @@
    -

    Usage

    +

    Usage +

    is_blank(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    object to check.

    -
    + +
    -

    Value

    +

    Value +

    Flag whether x is identical to an empty string, i.e. "".

    -

    Examples

    +

    Examples +

    is_blank("")
 #> [1] TRUE
 is_blank(" ")
@@ -95,17 +123,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/module_arguments.html b/latest-tag/reference/module_arguments.html index f92a768c..f250fde2 100644 --- a/latest-tag/reference/module_arguments.html +++ b/latest-tag/reference/module_arguments.html @@ -1,10 +1,26 @@ - -Standard Module Arguments — module_arguments • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -67,8 +89,10 @@
    -

    Arguments

    -
    data
    +

    Arguments +

    +
    +
    data

    (reactive)
    reactive(<teal_data>) holding all the data sets provided during app initialization after going through the filters.

    @@ -89,8 +113,11 @@

    ArgumentsArgumentsArguments

    teal.modules.hermes is a part of the NEST and pharmaverse.

    - + + - - + + diff --git a/latest-tag/reference/multiSampleVarSpecServer.html b/latest-tag/reference/multiSampleVarSpecServer.html index a4dd3341..b5b864d9 100644 --- a/latest-tag/reference/multiSampleVarSpecServer.html +++ b/latest-tag/reference/multiSampleVarSpecServer.html @@ -1,12 +1,28 @@ - - + + + + + +Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer • teal.modules.hermes +Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,13 +91,16 @@
    -

    Usage

    +

    Usage +

    multiSampleVarSpecServer(inputIds, original_data, ...)
    -

    Arguments

    -
    inputIds
    +

    Arguments +

    +
    +
    inputIds

    (character)
    multiple input IDs corresponding to the different sample variables specified in the UI function.

    @@ -93,9 +118,11 @@

    Arguments -

    Value

    +

    Value +

    List with the final transformed experiment_data reactive and a @@ -104,7 +131,8 @@

    Value

    -

    Examples

    +

    Examples +

    if (FALSE) {
 # In the server use:
 sample_var_specs <- multiSampleVarSpecServer(
@@ -122,17 +150,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/rADTTE.html b/latest-tag/reference/rADTTE.html index 473a496b..938c0d8e 100644 --- a/latest-tag/reference/rADTTE.html +++ b/latest-tag/reference/rADTTE.html @@ -1,8 +1,24 @@ - -Random Time to Event Analysis Dataset — rADTTE • teal.modules.hermes + + + + + + + + Skip to contents @@ -18,7 +34,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,31 +85,36 @@
    -

    Usage

    +

    Usage +

    rADTTE
    -

    Format

    +

    Format +

    An object of class tbl_df (inherits from tbl, data.frame) with 2000 rows and 67 columns.

    -

    Source

    +

    Source +

    internal

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/latest-tag/reference/sampleVarSpecInput.html b/latest-tag/reference/sampleVarSpecInput.html index cbd6fc77..6a611c1f 100644 --- a/latest-tag/reference/sampleVarSpecInput.html +++ b/latest-tag/reference/sampleVarSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Sample Variable Specification — sampleVarSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    sampleVarSpecInput(
   inputId,
   label_vars = "Select sample variable",
@@ -75,8 +98,10 @@ 
    Usage
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -88,20 +113,24 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    sampleVarSpecServer() for the module server and a complete example.

    -

    Examples

    +

    Examples +

    sampleVarSpecInput("my_vars", label_vars = "Select faceting variable")
 #> <div class="row">
 #>   <div class="col-sm-8">
@@ -141,17 +170,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/sampleVarSpecServer.html b/latest-tag/reference/sampleVarSpecServer.html index 8e9ea80b..5d102a7a 100644 --- a/latest-tag/reference/sampleVarSpecServer.html +++ b/latest-tag/reference/sampleVarSpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Sample Variable Specification — sampleVarSpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    sampleVarSpecServer(
   id,
   experiment_name,
@@ -81,8 +104,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -125,27 +150,32 @@

    Arguments -

    Value

    +

    Value +

    Reactive SummarizedExperiment::SummarizedExperiment which can be used as input for the relevant hermes functions.

    -

    Note

    +

    Note +

    Only atomic columns (e.g. not DataFrame columns) of the colData which are not completely missing (NA) will be shown for selection. If num_levels is specified then only factor columns will be available.

    -

    See also

    +

    See also +

    sampleVarSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id) {
   checkmate::assert_class(data, "teal_data")
   ns <- NS(id)
@@ -216,17 +246,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/teal.modules.hermes-package.html b/latest-tag/reference/teal.modules.hermes-package.html index 5a7c7fa5..a0d0a84c 100644 --- a/latest-tag/reference/teal.modules.hermes-package.html +++ b/latest-tag/reference/teal.modules.hermes-package.html @@ -1,10 +1,26 @@ - -teal.modules.hermes Package — teal.modules.hermes-package • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    +
    -

    teal.modules.hermes Package

    +

    +teal.modules.hermes Package

    Source: R/package.R
    teal.modules.hermes-package.Rd
    @@ -67,16 +90,24 @@
    -

    See also

    -

    Useful links:

    +
    -

    Author

    +

    Author +

    Maintainer: Daniel Sabanés Bové daniel.sabanes_bove@roche.com

    -

    Authors:

    • Nikolas Burkoff

      • +

      Authors:

      +
        +

      • Nikolas Burkoff

      • Dinakar Kulkarni

      • Konrad Pagacz

      • Namrata Bhatia

        • @@ -86,26 +117,32 @@

        Author<

      • Stefanie Bienert

      • Haocheng Li

      • Lyndsee Midori Zhang

        • -

      Other contributors:

      • Sorin Voicu [contributor]

        • +
      +

      Other contributors:

      +
        +

      • Sorin Voicu [contributor]

      • Benoit Falquet [contributor]

      • Mahmoud Hallal [contributor]

      • Tim Treis [contributor]

      • Vedha Viyash [contributor]

      • F. Hoffmann-La Roche AG [copyright holder, funder]

        • -
    + +
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/latest-tag/reference/tm_g_barplot.html b/latest-tag/reference/tm_g_barplot.html index c9c7b301..578ecf2c 100644 --- a/latest-tag/reference/tm_g_barplot.html +++ b/latest-tag/reference/tm_g_barplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Barplot — tm_g_barplot • teal.modules.hermes +Teal Module for RNA-seq Barplot — tm_g_barplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_barplot(
   label,
   mae_name,
@@ -96,8 +119,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -145,23 +170,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_barplot(): sets up the user interface.

      • +
        +

      • ui_g_barplot(): sets up the user interface.

      • srv_g_barplot(): sets up the server with reactive graph.

      • sample_tm_g_barplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -184,17 +215,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/tm_g_boxplot.html b/latest-tag/reference/tm_g_boxplot.html index 1a24f72b..8478cb54 100644 --- a/latest-tag/reference/tm_g_boxplot.html +++ b/latest-tag/reference/tm_g_boxplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Boxplot — tm_g_boxplot • teal.modules.hermes +Teal Module for RNA-seq Boxplot — tm_g_boxplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_boxplot(
   label,
   mae_name,
@@ -96,8 +119,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -145,23 +170,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_boxplot(): sets up the user interface.

      • +
        +

      • ui_g_boxplot(): sets up the user interface.

      • srv_g_boxplot(): sets up the server with reactive graph.

      • sample_tm_g_boxplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -184,17 +215,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/tm_g_forest_tte.html b/latest-tag/reference/tm_g_forest_tte.html index cc7b84e6..747c05d4 100644 --- a/latest-tag/reference/tm_g_forest_tte.html +++ b/latest-tag/reference/tm_g_forest_tte.html @@ -1,10 +1,26 @@ - -Teal Module for Survival Forest Plot — tm_g_forest_tte • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    tm_g_forest_tte(
   label,
   adtte_name,
@@ -109,8 +132,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -126,8 +151,11 @@

    ArgumentsArgumentsArguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_forest_tte(): sets up the user interface.

      • +
        +

      • ui_g_forest_tte(): sets up the user interface.

      • srv_g_forest_tte(): sets up the server with reactive graph.

      • sample_tm_g_forest_tte(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data()
 data <- within(data, {
   ADTTE <- teal.modules.hermes::rADTTE %>%
@@ -235,17 +270,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/tm_g_km.html b/latest-tag/reference/tm_g_km.html index 2c157c41..935e3a74 100644 --- a/latest-tag/reference/tm_g_km.html +++ b/latest-tag/reference/tm_g_km.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for Kaplan-Meier Plot — tm_g_km • teal.modules.hermes +Teal Module for Kaplan-Meier Plot — tm_g_km • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_km(
   label,
   adtte_name,
@@ -101,8 +124,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -118,8 +143,11 @@

    ArgumentsArgumentsArguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_km(): sets up the user interface.

      • +
        +

      • ui_g_km(): sets up the user interface.

      • srv_g_km(): sets up the user interface.

      • sample_tm_g_km(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data()
 data <- within(data, {
   ADTTE <- teal.modules.hermes::rADTTE %>%
@@ -221,17 +256,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/tm_g_pca.html b/latest-tag/reference/tm_g_pca.html index d55d9368..d4885190 100644 --- a/latest-tag/reference/tm_g_pca.html +++ b/latest-tag/reference/tm_g_pca.html @@ -1,14 +1,30 @@ - - + + + + + +Teal Module for PCA Analysis — tm_g_pca • teal.modules.hermes +Teal Module for PCA Analysis — tm_g_pca • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,7 +94,8 @@
    -

    Usage

    +

    Usage +

    tm_g_pca(
   label,
   mae_name,
@@ -89,8 +112,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -132,23 +157,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_pca(): sets up the user interface.

      • +
        +

      • ui_g_pca(): sets up the user interface.

      • srv_g_pca(): sets up the server with reactive graph.

      • sample_tm_g_pca(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -171,17 +202,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/tm_g_quality.html b/latest-tag/reference/tm_g_quality.html index 222430a5..3a7b7232 100644 --- a/latest-tag/reference/tm_g_quality.html +++ b/latest-tag/reference/tm_g_quality.html @@ -1,14 +1,30 @@ - - + + + + + +Teal Module for RNA-seq Quality Control — tm_g_quality • teal.modules.hermes +Teal Module for RNA-seq Quality Control — tm_g_quality • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,7 +94,8 @@
    -

    Usage

    +

    Usage +

    tm_g_quality(
   label,
   mae_name,
@@ -89,8 +112,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -132,23 +157,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_quality(): sets up the user interface.

      • +
        +

      • ui_g_quality(): sets up the user interface.

      • srv_g_quality(): sets up the server with reactive graphs.

      • sample_tm_g_quality(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -170,17 +201,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/tm_g_scatterplot.html b/latest-tag/reference/tm_g_scatterplot.html index f11189c6..cbb7a0b1 100644 --- a/latest-tag/reference/tm_g_scatterplot.html +++ b/latest-tag/reference/tm_g_scatterplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Scatterplot — tm_g_scatterplot • teal.modules.hermes +Teal Module for RNA-seq Scatterplot — tm_g_scatterplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_scatterplot(
   label,
   mae_name,
@@ -96,8 +119,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -145,23 +170,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_scatterplot(): sets up the user interface.

      • +
        +

      • ui_g_scatterplot(): sets up the user interface.

      • srv_g_scatterplot(): sets up the server with reactive graph.

      • sample_tm_g_scatterplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -184,17 +215,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/tm_g_volcanoplot.html b/latest-tag/reference/tm_g_volcanoplot.html index 51b4f97f..e6f185bd 100644 --- a/latest-tag/reference/tm_g_volcanoplot.html +++ b/latest-tag/reference/tm_g_volcanoplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot • teal.modules.hermes +Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_volcanoplot(
   label,
   mae_name,
@@ -93,8 +116,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -136,23 +161,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_volcanoplot(): sets up the user interface.

      • +
        +

      • ui_g_volcanoplot(): sets up the user interface.

      • srv_g_volcanoplot(): sets up the server with reactive graph.

      • sample_tm_g_volcanoplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -175,17 +206,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/latest-tag/reference/top_gene_plot.html b/latest-tag/reference/top_gene_plot.html index 4897a425..990084a9 100644 --- a/latest-tag/reference/top_gene_plot.html +++ b/latest-tag/reference/top_gene_plot.html @@ -1,10 +1,26 @@ - -Most Expressed Genes Plot — top_gene_plot • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,46 +88,54 @@
    -

    Usage

    +

    Usage +

    top_gene_plot(object, assay_name)
    -

    Arguments

    -
    object
    +

    Arguments +

    +
    +
    object

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    assay_name

    (string)
    the assay to define the groups.

    -
    + +
    -

    Value

    +

    Value +

    Plot to be displayed in the teal app.

    -

    Examples

    +

    Examples +

    library(hermes)
 object <- HermesData(summarized_experiment)
 result <- top_gene_plot(object, assay_name = "counts")
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/latest-tag/reference/validate_gene_spec.html b/latest-tag/reference/validate_gene_spec.html index 4dabc496..031b536f 100644 --- a/latest-tag/reference/validate_gene_spec.html +++ b/latest-tag/reference/validate_gene_spec.html @@ -1,12 +1,28 @@ - - + + + + + +Validation of Gene Specification — validate_gene_spec • teal.modules.hermes +Validation of Gene Specification — validate_gene_spec • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,33 +91,39 @@
    -

    Usage

    +

    Usage +

    validate_gene_spec(gene_spec, gene_choices)
    -

    Arguments

    -
    gene_spec
    +

    Arguments +

    +
    +
    gene_spec

    (GeneSpec)
    gene specification.

    gene_choices

    (character)
    all possible gene choices.

    -
    + + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/latest-tag/reference/validate_n_levels.html b/latest-tag/reference/validate_n_levels.html index 7fa7be99..3922838b 100644 --- a/latest-tag/reference/validate_n_levels.html +++ b/latest-tag/reference/validate_n_levels.html @@ -1,12 +1,28 @@ - - + + + + + +Validation of Number of Levels — validate_n_levels • teal.modules.hermes +Validation of Number of Levels — validate_n_levels • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,13 +91,16 @@
    -

    Usage

    +

    Usage +

    validate_n_levels(x, name, n_levels)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (factor)
    factor to validate.

    @@ -86,20 +111,23 @@

    Arguments

    + + + + - - + + diff --git a/main/404.html b/main/404.html index eb3ba339..88cb30c0 100644 --- a/main/404.html +++ b/main/404.html @@ -1,5 +1,4 @@ - - + @@ -34,7 +33,17 @@
  • Reference
  • Articles
  • Changelog
    • - + +
    diff --git a/main/CODE_OF_CONDUCT.html b/main/CODE_OF_CONDUCT.html index aa7e8390..87ced7f4 100644 --- a/main/CODE_OF_CONDUCT.html +++ b/main/CODE_OF_CONDUCT.html @@ -1,5 +1,19 @@ - -Contributor Covenant Code of Conduct • teal.modules.hermes + + + + + + +Contributor Covenant Code of Conduct • teal.modules.hermes + + + + + + + + + Skip to contents @@ -15,11 +29,25 @@ + + +
      +
      • +
    + @@ -34,65 +62,80 @@

    Contributor Covenant Code of Conduct

    -

    Our Pledge

    +

    Our Pledge +

    We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.

    We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.

    -

    Our Standards

    +

    Our Standards +

    Examples of behavior that contributes to a positive environment for our community include:

    -
    • Demonstrating empathy and kindness toward other people
      • +
        +
      • Demonstrating empathy and kindness toward other people
      • Being respectful of differing opinions, viewpoints, and experiences
      • Giving and gracefully accepting constructive feedback
      • Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
      • Focusing on what is best not just for us as individuals, but for the overall community
        • -

      Examples of unacceptable behavior include:

      -
      • The use of sexualized language or imagery, and sexual attention or advances of any kind
        • +
      +

      Examples of unacceptable behavior include:

      +
        +
      • The use of sexualized language or imagery, and sexual attention or advances of any kind
      • Trolling, insulting or derogatory comments, and personal or political attacks
      • Public or private harassment
      • Publishing others’ private information, such as a physical or email address, without their explicit permission
      • Other conduct which could reasonably be considered inappropriate in a professional setting
        • -
    + +
    -

    Enforcement Responsibilities

    +

    Enforcement Responsibilities +

    Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.

    Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.

    -

    Scope

    +

    Scope +

    This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.

    -

    Enforcement

    +

    Enforcement +

    Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at [INSERT CONTACT METHOD]. All complaints will be reviewed and investigated promptly and fairly.

    All community leaders are obligated to respect the privacy and security of the reporter of any incident.

    -

    Enforcement Guidelines

    +

    Enforcement Guidelines +

    Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:

    -

    1. Correction

    +

    1. Correction +

    Community Impact: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.

    Consequence: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.

    -

    2. Warning

    +

    2. Warning +

    Community Impact: A violation through a single incident or series of actions.

    Consequence: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.

    -

    3. Temporary Ban

    +

    3. Temporary Ban +

    Community Impact: A serious violation of community standards, including sustained inappropriate behavior.

    Consequence: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.

    -

    4. Permanent Ban

    +

    4. Permanent Ban +

    Community Impact: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.

    Consequence: A permanent ban from any sort of public interaction within the community.

    -

    Attribution

    +

    Attribution +

    This Code of Conduct is adapted from the Contributor Covenant, version 2.1, available at https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.

    Community Impact Guidelines were inspired by Mozilla’s code of conduct enforcement ladder.

    For answers to common questions about this code of conduct, see the FAQ at https://www.contributor-covenant.org/faq. Translations are available at https://www.contributor-covenant.org/translations.

    @@ -100,17 +143,19 @@

    Attribution

    + + - + + - + + diff --git a/main/CONTRIBUTING.html b/main/CONTRIBUTING.html index f8f8e968..38090b08 100644 --- a/main/CONTRIBUTING.html +++ b/main/CONTRIBUTING.html @@ -1,5 +1,19 @@ - -Contribution Guidelines • teal.modules.hermes + + + + + + +Contribution Guidelines • teal.modules.hermes + + + + + + + + + Skip to contents @@ -15,11 +29,25 @@ + + +
      +
      • +
    + @@ -36,7 +64,8 @@

    Contribution Guidelines

    🙏 Thank you for taking the time to contribute!

    Your input is deeply valued, whether an issue, a pull request, or even feedback, regardless of size, content or scope.

    -

    Table of contents

    +

    Table of contents +

    👶 Getting started

    📔 Code of Conduct

    🗃 License

    @@ -47,38 +76,47 @@

    Table of contents❓ Questions

    -

    Getting started

    +

    Getting started +

    Please refer the project documentation for a brief introduction. Please also see other articles within the project documentation for additional information.

    -

    Code of Conduct

    +

    Code of Conduct +

    A Code of Conduct governs this project. Participants and contributors are expected to follow the rules outlined therein.

    -

    License

    +

    License +

    All your contributions will be covered by this project’s license.

    -

    Issues

    +

    Issues +

    We use GitHub to track issues, feature requests, and bugs. Before submitting a new issue, please check if the issue has already been reported. If the issue already exists, please upvote the existing issue 👍.

    For new feature requests, please elaborate on the context and the benefit the feature will have for users, developers, or other relevant personas.

    -

    Pull requests

    +

    Pull requests +

    -

    GitHub Flow

    +

    GitHub Flow +

    This repository uses the GitHub Flow model for collaboration. To submit a pull request:

    -
    1. +
        +

      1. Create a branch

        Please see the branch naming convention below. If you don’t have write access to this repository, please fork it.

      2. Make changes

        Make sure your code

        -
        • passes all checks imposed by GitHub Actions
          • +
            +
          • passes all checks imposed by GitHub Actions
          • is well documented
          • is well tested with unit tests sufficiently covering the changes introduced
            • -
          +
        +

      3. Create a pull request (PR)

        In the pull request description, please link the relevant issue (if any), provide a detailed description of the change, and include any assumptions.

        @@ -92,76 +130,93 @@

        GitHub Flow -

        Branch naming convention

        +

        Branch naming convention +

        Suppose your changes are related to a current issue in the current project; please name your branch as follows: <issue_id>_<short_description>. Please use underscore (_) as a delimiter for word separation. For example, 420_fix_ui_bug would be a suitable branch name if your change is resolving and UI-related bug reported in issue number 420 in the current project.

        If your change affects multiple repositories, please name your branches as follows: <issue_id>_<issue_repo>_<short description>. For example, 69_awesomeproject_fix_spelling_error would reference issue 69 reported in project awesomeproject and aims to resolve one or more spelling errors in multiple (likely related) repositories.

    monorepo and staged.dependencies -

    + +

    Sometimes you might need to change upstream dependent package(s) to be able to submit a meaningful change. We are using staged.dependencies functionality to simulate a monorepo behavior. The dependency configuration is already specified in this project’s staged_dependencies.yaml file. You need to name the feature branches appropriately. This is the only exception from the branch naming convention described above.

    Please refer to the staged.dependencies package documentation for more details.

    -

    Coding guidelines

    +

    Coding guidelines +

    This repository follows some unified processes and standards adopted by its maintainers to ensure software development is carried out consistently within teams and cohesively across other repositories.

    -

    Style guide

    +

    Style guide +

    This repository follows the standard tidyverse style guide and uses lintr for lint checks. Customized lint configurations are available in this repository’s .lintr file.

    -

    Dependency management

    +

    Dependency management +

    Lightweight is the right weight. This repository follows tinyverse recommedations of limiting dependencies to minimum.

    -

    Dependency version management

    +

    Dependency version management +

    If the code is not compatible with all (!) historical versions of a given dependenct package, it is required to specify minimal version in the DESCRIPTION file. In particular: if the development version requires (imports) the development version of another package - it is required to put abc (>= 1.2.3.9000).

    -

    Recommended development environment & tools

    +

    Recommended development environment & tools +

    -

    R & package versions

    +

    R & package versions +

    We continuously test our packages against the newest R version along with the most recent dependencies from CRAN and BioConductor. We recommend that your working environment is also set up in the same way. You can find the details about the R version and packages used in the R CMD check GitHub Action execution log - there is a step that prints out the R sessionInfo().

    If you discover bugs on older R versions or with an older set of dependencies, please create the relevant bug reports.

    -

    pre-commit

    +

    +pre-commit +

    We highly recommend that you use the pre-commit tool combined with R hooks for pre-commit to execute some of the checks before committing and pushing your changes.

    Pre-commit hooks are already available in this repository’s .pre-commit-config.yaml file.

    -

    Recognition model

    +

    Recognition model +

    As mentioned previously, all contributions are deeply valued and appreciated. While all contribution data is available as part of the repository insights, to recognize a significant contribution and hence add the contributor to the package authors list, the following rules are enforced:

    -
    • Minimum 5% of lines of code authored* (determined by git blame query) OR
      • +
        +
      • Minimum 5% of lines of code authored* (determined by git blame query) OR
      • Being at the top 5 contributors in terms of number of commits OR lines added OR lines removed*
        • -

      *Excluding auto-generated code, including but not limited to roxygen comments or renv.lock files.

      +
    +

    *Excluding auto-generated code, including but not limited to roxygen comments or renv.lock files.

    The package maintainer also reserves the right to adjust the criteria to recognize contributions.

    -

    Questions

    +

    Questions +

    If you have further questions regarding the contribution guidelines, please contact the package/repository maintainer.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/LICENSE-text.html b/main/LICENSE-text.html index 8cda01cc..6a18a13a 100644 --- a/main/LICENSE-text.html +++ b/main/LICENSE-text.html @@ -1,5 +1,19 @@ - -License • teal.modules.hermes + + + + + + +License • teal.modules.hermes + + + + + + + + + Skip to contents @@ -15,11 +29,25 @@ + + +
      +
      • +
    + @@ -46,17 +74,19 @@

    License

    limitations under the License. - + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/SECURITY.html b/main/SECURITY.html index d3bf1a8a..79c65693 100644 --- a/main/SECURITY.html +++ b/main/SECURITY.html @@ -1,5 +1,19 @@ - -Security Policy • teal.modules.hermes + + + + + + +Security Policy • teal.modules.hermes + + + + + + + + + Skip to contents @@ -15,11 +29,25 @@ + + +
      +
      • +
    + @@ -34,38 +62,44 @@

    Security Policy

    -

    Reporting Security Issues

    +

    Reporting Security Issues +

    If you believe you have found a security vulnerability in any of the repositories in this organization, please report it to us through coordinated disclosure.

    Please do not report security vulnerabilities through public GitHub issues, discussions, or pull requests.

    Instead, please send an email to vulnerability.management[@]roche.com.

    Please include as much of the information listed below as you can to help us better understand and resolve the issue:

    -
    • The type of issue (e.g., buffer overflow, SQL injection, or cross-site scripting)
      • +
        +
      • The type of issue (e.g., buffer overflow, SQL injection, or cross-site scripting)
      • Full paths of source file(s) related to the manifestation of the issue
      • The location of the affected source code (tag/branch/commit or direct URL)
      • Any special configuration required to reproduce the issue
      • Step-by-step instructions to reproduce the issue
      • Proof-of-concept or exploit code (if possible)
      • Impact of the issue, including how an attacker might exploit the issue
        • -

      This information will help us triage your report more quickly.

      +
    +

    This information will help us triage your report more quickly.

    -

    Data Security Standards (DSS)

    +

    Data Security Standards (DSS) +

    Please make sure that while reporting issues in the form a bug, feature, or pull request, all sensitive information such as PII, PHI, and PCI is completely removed from any text and attachments, including pictures and videos.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/articles/Getting_Started.html b/main/articles/Getting_Started.html index a7aee36a..88b3e10e 100644 --- a/main/articles/Getting_Started.html +++ b/main/articles/Getting_Started.html @@ -1,5 +1,4 @@ - - + @@ -34,7 +33,17 @@
  • Reference
  • Articles
  • Changelog
    • - + +
    diff --git a/main/articles/index.html b/main/articles/index.html index b4c377f5..45bec66b 100644 --- a/main/articles/index.html +++ b/main/articles/index.html @@ -1,5 +1,19 @@ - -Articles • teal.modules.hermes + + + + + + +Articles • teal.modules.hermes + + + + + + + + + Skip to contents @@ -15,11 +29,25 @@ + + +
      +
      • +
    + @@ -34,20 +62,25 @@

    Articles

    All vignettes

    -
    Getting Started
    +
    +
    Getting Started
    -
    - + +
    + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/authors.html b/main/authors.html index 5f1f1ea4..3251aa29 100644 --- a/main/authors.html +++ b/main/authors.html @@ -1,5 +1,19 @@ - -Authors and Citation • teal.modules.hermes + + + + + + +Authors and Citation • teal.modules.hermes + + + + + + + + + Skip to contents @@ -15,11 +29,25 @@ + + +
      +
      • +
    + @@ -33,7 +61,8 @@

    Authors and Citation

    Authors

    -
    • +
        +

      • Dony Unardi. Maintainer.

        • @@ -105,7 +134,8 @@

        Authors

        F. Hoffmann-La Roche AG. Copyright holder, funder.

        -
    + +

    Citation

    @@ -127,17 +157,19 @@

    Citation

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/index.html b/main/index.html index a38f6c09..f88be425 100644 --- a/main/index.html +++ b/main/index.html @@ -1,5 +1,4 @@ - - + @@ -36,7 +35,17 @@
  • Reference
  • Articles
  • Changelog
    • - + +
    diff --git a/main/news/index.html b/main/news/index.html index 6de90a18..8d073905 100644 --- a/main/news/index.html +++ b/main/news/index.html @@ -1,5 +1,19 @@ - -Changelog • teal.modules.hermes + + + + + + +Changelog • teal.modules.hermes + + + + + + + + + Skip to contents @@ -15,11 +29,25 @@ + + +
      +
      • +
    + @@ -32,79 +60,120 @@

    Changelog

    -

    teal.modules.hermes 0.1.6.9024

    +

    teal.modules.hermes 0.1.6.9024 +

    -

    Miscellaneous

    -
    • Added placeholders for assaySpec, adtteSpec and geneSpec inputs when no option is selected.
      • +

      Miscellaneous +

      +
        +
      • Added placeholders for assaySpec, adtteSpec and geneSpec inputs when no option is selected.
      • Disabled the select input for assaySpec and adtteSpec when there are no options available.
      • For module developers: The module gets teal_data object in the UI and reactive(<teal_data>) in the server
        • -
    + +
    -

    Enhancements

    -
    • Updated the documentation and vignettes with the new way of specifying data for teal::init(). The data argument accepts teal_data object.
      • +

      Enhancements +

      +
        +
      • Updated the documentation and vignettes with the new way of specifying data for teal::init(). The data argument accepts teal_data object.
      • Added teal.logger functionality for logging changes in shiny inputs in all modules.
        • -
    + +
    -

    teal.modules.hermes 0.1.5

    +

    teal.modules.hermes 0.1.5 +

    -

    Bug Fixes

    -
    • Filtering data with the filter panel now correctly triggers the sampleVarSpecModule.
      • -
    +

    Bug Fixes +

    +
      +
    • Filtering data with the filter panel now correctly triggers the sampleVarSpecModule.
      • +
    +
    -

    Breaking changes

    -
    • Replaced datasets argument containing FilteredData with the new arguments data (tdata object) and filter_panel_api (FilterPanelAPI).
      • -
    +

    Breaking changes +

    +
      +
    • Replaced datasets argument containing FilteredData with the new arguments data (tdata object) and filter_panel_api (FilterPanelAPI).
      • +
    +
    -

    Miscellaneous

    -
    • Removed scda from dependencies.
      • +

      Miscellaneous +

      +
        +
      • Removed scda from dependencies.
      • Migrate to shinytest2.
        • -
    + +
    -

    teal.modules.hermes 0.1.4

    -
    • Added the teal.reporter functionality to all modules.
      • +

      teal.modules.hermes 0.1.4 +

      +
        +
      • Added the teal.reporter functionality to all modules.
      • Add installation instruction
        • -
    + +
    -

    teal.modules.hermes 0.1.3

    -
    • Improve the selection of sample variables in the forest module (tm_g_forest_tte) such that only categorical variables can be selected in the first place.
      • -
    -

    Miscellaneous

    -
    • Added a template to the pkgdown site.
      • +

      teal.modules.hermes 0.1.3 +

      +
        +
      • Improve the selection of sample variables in the forest module (tm_g_forest_tte) such that only categorical variables can be selected in the first place.
        • +
      +
      +

      Miscellaneous +

      +
        +
      • Added a template to the pkgdown site.
      • Updated package authors.
      • Added the option categorical_only to the sampleVarSpec server module, which allows to only show categorical sample variables for selection.
        • -
      +
    +
    -

    teal.modules.hermes 0.1.2

    -
    • Rewrote modules to use moduleServer and updated call to plot_with_settings_srv after changes in teal.devel.
      • +

      teal.modules.hermes 0.1.2 +

      +
        +
      • Rewrote modules to use moduleServer and updated call to plot_with_settings_srv after changes in teal.devel.
      • Replaced calls to teal::root_modules with teal::modules following deprecation of teal::root_modules.
      • Added basic logging to the modules.
      • Fixed the geneSpecInput so that the hermes app doesn’t fail anymore (on chrome) on an experiment with no genes.
        • -
    + +
    -

    teal.modules.hermes 0.1.1

    +

    teal.modules.hermes 0.1.1 +

    -

    Bug Fixes

    -
    • Updated legend for the PCA plot.
      • +

      Bug Fixes +

      +
        +
      • Updated legend for the PCA plot.
      • Gene selection with more than a few thousand genes no longer hangs the application. This is achieved through a different selection input in the corresponding geneSpec shiny module.
      • Only atomic columns of colData with at least one value can now be selected in the sampleVarSpecModule.
        • -
    + +
    -

    Miscellaneous

    -
    • Updated R version requirement to >= 3.6.
      • +

      Miscellaneous +

      +
        +
      • Updated R version requirement to >= 3.6.
      • Updated sampleVarSpec and geneSpec modules with new icons to remove warnings when using shiny version >= 1.7.
      • Removed dependencies on deprecated packages utils.nest and test.nest.
        • -
    + +
    -

    teal.modules.hermes 0.1.0

    -
    • First release of the teal.modules.hermes package, which contains teal modules for RNA-seq analysis using the hermes package.
      • +

      teal.modules.hermes 0.1.0 +

      +
        +
      • First release of the teal.modules.hermes package, which contains teal modules for RNA-seq analysis using the hermes package.
      • New users should first begin by reading the README.md of the teal.modules.hermes package to become familiar.
        • -
      -

      New Features

      -
      • +
      +
      +

      New Features +

      +
      +
    +
    + + - + + - + + diff --git a/main/reference/adtteSpecInput.html b/main/reference/adtteSpecInput.html index 6e51aca2..130c4ff1 100644 --- a/main/reference/adtteSpecInput.html +++ b/main/reference/adtteSpecInput.html @@ -1,7 +1,23 @@ - -Module Input for ADTTE Specification — adtteSpecInput • teal.modules.hermes + + + + + + +Module Input for ADTTE Specification — adtteSpecInput • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -40,44 +70,54 @@

    Module Input for ADTTE Specification

    -

    Usage

    +

    Usage +

    adtteSpecInput(inputId, label_paramcd = "Select Endpoint")
    -

    Arguments

    +

    Arguments +

    -
    inputId
    +
    +
    inputId +

    (string)
    the ID used to call the module input.

    -
    label_paramcd
    +
    label_paramcd +

    (string)
    label for the endpoint (PARAMCD) selection.

    -
    + +
    -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    adtteSpecServer() for the module server and a complete example.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/reference/adtteSpecServer.html b/main/reference/adtteSpecServer.html index 2949db94..76043cbc 100644 --- a/main/reference/adtteSpecServer.html +++ b/main/reference/adtteSpecServer.html @@ -1,15 +1,31 @@ - -Module Server for ADTTE Specification — adtteSpecServer • teal.modules.hermes + + + + + +Module Server for ADTTE Specification — adtteSpecServer • teal.modules.hermes + + + + + + + +the numeric column according to the quantile cutoffs specified in probs."> + + + + Skip to contents @@ -25,11 +41,25 @@ + + +
      +
      • +
    + @@ -52,7 +82,8 @@

    Module Server for ADTTE Specification

    -

    Usage

    +

    Usage +

    adtteSpecServer(
   id,
   data,
@@ -68,31 +99,41 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    id
    +
    +
    id +

    (string) the shiny module id.

    -
    data
    +
    data +

    (reactive)
    reactive(<teal_data>) holding all the data sets provided during app initialization after going through the filters.

    -
    mae_name
    +
    mae_name +

    (string)
    name of the MAE data used in the teal module.

    -
    adtte_name
    +
    adtte_name +

    (string)
    name of the ADTTE dataset.

    -
    adtte_vars
    -

    (named list of string)
    -names of the variables to use in the ADTTE dataset. It should comprise elements:

    • aval: the numeric time-to-event variable.

      • +
      adtte_vars +
      +
      +

      (named list of string)
      +names of the variables to use in the ADTTE dataset. It should comprise elements:

      +
        +

      • aval: the numeric time-to-event variable.

      • avalu: the variable holding the unit of aval.

      • is_event: the logical event variable. It needs to be TRUE when there was an observed event, and FALSE if the time is censored without @@ -100,45 +141,58 @@

        Argumentsexperiment_data +
        experiment_data +

        (reactive AnyHermesData)
        input experiment.

        -
        experiment_name
        +
        experiment_name +

        (reactive string)
        name of the input experiment.

        -
        assay
        +
        assay +

        (reactive string)
        name of the assay.

        -
        genes
        +
        genes +

        (reactive GeneSpec)
        gene specification.

        -
        probs
        +
        probs +

        (reactive numeric)
        probabilities to bin the gene or gene signature into.

        -

    + +
    -

    Value

    -

    List with the following elements:

    • binned_adtte_subset: reactive containing the joined ADTTE and gene data.

      • +

      Value +

      +

      List with the following elements:

      +
        +

      • binned_adtte_subset: reactive containing the joined ADTTE and gene data.

      • gene_col: reactive containing the string with the column name of the original numeric gene variable.

      • gene_factor: string with the variable name for the binned gene data.

      • time_unit: reactive string with the time unit for the current subset.

        • -
    + +
    -

    See also

    +

    See also +

    adtteSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    library(dplyr)
 #> 
 #> Attaching package: ‘dplyr’
@@ -247,17 +301,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/assaySpecInput.html b/main/reference/assaySpecInput.html index ec28e704..6bbe0181 100644 --- a/main/reference/assaySpecInput.html +++ b/main/reference/assaySpecInput.html @@ -1,7 +1,23 @@ - -Module Input for Assay Specification — assaySpecInput • teal.modules.hermes + + + + + + +Module Input for Assay Specification — assaySpecInput • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -40,44 +70,54 @@

    Module Input for Assay Specification

    -

    Usage

    +

    Usage +

    assaySpecInput(inputId, label_assays = "Select Assay")
    -

    Arguments

    +

    Arguments +

    -
    inputId
    +
    +
    inputId +

    (string)
    the ID used to call the module input.

    -
    label_assays
    +
    label_assays +

    (string)
    label for the assay selection.

    -
    + +
    -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    assaySpecServer() for the module server and a complete example.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/reference/assaySpecServer.html b/main/reference/assaySpecServer.html index fecc0fa9..ee2b4851 100644 --- a/main/reference/assaySpecServer.html +++ b/main/reference/assaySpecServer.html @@ -1,7 +1,23 @@ - -Module Server for Assay Specification — assaySpecServer • teal.modules.hermes + + + + + + +Module Server for Assay Specification — assaySpecServer • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -40,38 +70,48 @@

    Module Server for Assay Specification

    -

    Usage

    +

    Usage +

    assaySpecServer(id, assays, exclude_assays = character())
    -

    Arguments

    +

    Arguments +

    -
    id
    +
    +
    id +

    (string) the shiny module id.

    -
    assays
    +
    assays +

    (reactive character)
    available assays in the currently selected experiment.

    -
    exclude_assays
    +
    exclude_assays +

    (character)
    names of the assays which should not be included in choices in the teal module.

    -
    + +
    -

    Value

    +

    Value +

    The chosen assay as a reactive string.

    -

    See also

    +

    See also +

    assaySpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id) {
   ns <- NS(id)
   teal.widgets::standard_layout(
@@ -129,17 +169,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/assert_adtte_vars.html b/main/reference/assert_adtte_vars.html index 54c11132..b387c544 100644 --- a/main/reference/assert_adtte_vars.html +++ b/main/reference/assert_adtte_vars.html @@ -1,7 +1,23 @@ - -Check for ADTTE Variables — assert_adtte_vars • teal.modules.hermes + + + + + + +Check for ADTTE Variables — assert_adtte_vars • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -40,40 +70,49 @@

    Check for ADTTE Variables

    -

    Usage

    +

    Usage +

    assert_adtte_vars(x)
    -

    Arguments

    +

    Arguments +

    -
    x
    +
    +
    x +

    an object to check.

    -
    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    assert_adtte_vars(list(aval = "AV", is_event = "EV", paramcd = "PC", usubjid = "ID", avalu = "u"))
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/reference/assert_summary_funs.html b/main/reference/assert_summary_funs.html index 65b07ddd..6c69e105 100644 --- a/main/reference/assert_summary_funs.html +++ b/main/reference/assert_summary_funs.html @@ -1,7 +1,23 @@ - -Check for List of Summary Functions — assert_summary_funs • teal.modules.hermes + + + + + + +Check for List of Summary Functions — assert_summary_funs • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -40,45 +70,55 @@

    Check for List of Summary Functions

    -

    Usage

    +

    Usage +

    assert_summary_funs(x, null.ok = FALSE)
    -

    Arguments

    +

    Arguments +

    -
    x
    +
    +
    x +

    an object to check.

    -
    null.ok
    +
    null.ok +

    (flag)
    whether x may also contain NULL, meaning that a user choice is possible where no summary function should be applied.

    -
    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    assert_summary_funs(list(mean = colMeans, raw = NULL), null.ok = TRUE)
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/reference/assertion_arguments.html b/main/reference/assertion_arguments.html index ede57734..7978b04f 100644 --- a/main/reference/assertion_arguments.html +++ b/main/reference/assertion_arguments.html @@ -1,7 +1,23 @@ - -Standard Assertion Arguments — assertion_arguments • teal.modules.hermes + + + + + + +Standard Assertion Arguments — assertion_arguments • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -41,49 +71,60 @@

    Standard Assertion Arguments

    -

    Arguments

    +

    Arguments +

    -
    x
    +
    +
    x +

    an object to check.

    -
    null.ok
    +
    null.ok +

    (flag)
    whether x may also be NULL.

    -
    .var.name
    +
    .var.name +

    (string)
    name of the checked object to print in assertions; defaults to the heuristic implemented in checkmate::vname().

    -
    add
    +
    add +

    (AssertCollection or NULL)
    collection to store assertion messages, see checkmate::AssertCollection.

    -
    info
    +
    info +

    (string)
    extra information to be included in the message for the testthat reporter, see testthat::expect_that().

    -
    label
    +
    label +

    (string)
    name of the checked object to print in messages. Defaults to the heuristic implemented in checkmate::vname().

    -
    + + - + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/reference/assertions.html b/main/reference/assertions.html index 71abb142..548ed20b 100644 --- a/main/reference/assertions.html +++ b/main/reference/assertions.html @@ -1,11 +1,27 @@ - -Additional Assertions for checkmate — assertions • teal.modules.hermes + + + + + +Additional Assertions for checkmate — assertions • teal.modules.hermes + + + + + + + +linked below."> + + + + Skip to contents @@ -21,11 +37,25 @@ + + +
      +
      • +
    + @@ -33,7 +63,8 @@
    -

    Additional Assertions for checkmate

    +

    Additional Assertions for checkmate +

    Source: R/checkmate.R
    assertions.Rd
    @@ -47,30 +78,37 @@

    Additional Assertions for checkmate

    -

    Value

    -

    Depending on the function prefix.

    • assert_ functions return the object invisibly if successful, and otherwise +

      Value +

      +

      Depending on the function prefix.

      +
        +

      • assert_ functions return the object invisibly if successful, and otherwise throw an error message.

      • check_ functions return TRUE if successful, otherwise a string with the error message.

      • test_ functions just return TRUE or FALSE.

        • -
    + +
    -

    See also

    +

    See also +

    assert_tag(), assert_reactive(), assert_summary_funs(), assert_adtte_vars()

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/reference/check_reactive.html b/main/reference/check_reactive.html index 7a96c7c8..438ed3f7 100644 --- a/main/reference/check_reactive.html +++ b/main/reference/check_reactive.html @@ -1,7 +1,23 @@ - -Check for Reactive Input — check_reactive • teal.modules.hermes + + + + + + +Check for Reactive Input — check_reactive • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -40,7 +70,8 @@

    Check for Reactive Input

    -

    Usage

    +

    Usage +

    check_reactive(x)
 
 assert_reactive(x, .var.name = checkmate::vname(x), add = NULL)
@@ -49,30 +80,38 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    x
    +
    +
    x +

    an object to check.

    -
    .var.name
    +
    .var.name +

    (string)
    name of the checked object to print in assertions; defaults to the heuristic implemented in checkmate::vname().

    -
    add
    +
    add +

    (AssertCollection or NULL)
    collection to store assertion messages, see checkmate::AssertCollection.

    -
    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    check_reactive("bla")
 #> [1] FALSE
 check_reactive(reactive("bla"))
@@ -80,17 +119,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/check_tag.html b/main/reference/check_tag.html index d239bc7a..4c4f9899 100644 --- a/main/reference/check_tag.html +++ b/main/reference/check_tag.html @@ -1,7 +1,23 @@ - -Check for Shiny Tag — check_tag • teal.modules.hermes + + + + + + +Check for Shiny Tag — check_tag • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -40,7 +70,8 @@

    Check for Shiny Tag

    -

    Usage

    +

    Usage +

    check_tag(x, null.ok = FALSE)
 
 assert_tag(x, null.ok = FALSE, .var.name = checkmate::vname(x), add = NULL)
@@ -51,44 +82,55 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    x
    +
    +
    x +

    an object to check.

    -
    null.ok
    +
    null.ok +

    (flag)
    whether x may also be NULL.

    -
    .var.name
    +
    .var.name +

    (string)
    name of the checked object to print in assertions; defaults to the heuristic implemented in checkmate::vname().

    -
    add
    +
    add +

    (AssertCollection or NULL)
    collection to store assertion messages, see checkmate::AssertCollection.

    -
    info
    +
    info +

    (string)
    extra information to be included in the message for the testthat reporter, see testthat::expect_that().

    -
    label
    +
    label +

    (string)
    name of the checked object to print in messages. Defaults to the heuristic implemented in checkmate::vname().

    -
    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    check_tag("bla")
 #> [1] "Must be a 'shiny.tag' or NULL"
 check_tag(NULL, null.ok = TRUE)
@@ -96,17 +138,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/experimentSpecInput.html b/main/reference/experimentSpecInput.html index e989282b..6b088286 100644 --- a/main/reference/experimentSpecInput.html +++ b/main/reference/experimentSpecInput.html @@ -1,7 +1,23 @@ - -Module Input for Experiment Specification — experimentSpecInput • teal.modules.hermes + + + + + + +Module Input for Experiment Specification — experimentSpecInput • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -40,7 +70,8 @@

    Module Input for Experiment Specification

    -

    Usage

    +

    Usage +

    experimentSpecInput(
   inputId,
   data,
@@ -50,49 +81,60 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    inputId
    +
    +
    inputId +

    (string)
    the ID used to call the module input.

    -
    data
    +
    data +

    (reactive)
    reactive(<teal_data>) holding all the data sets provided during app initialization after going through the filters.

    -
    mae_name
    +
    mae_name +

    (string)
    name of the MAE data used in the teal module.

    -
    label_experiments
    +
    label_experiments +

    (string)
    label for the experiment selection.

    -
    + +
    -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    experimentSpecServer() for the module server and a complete example.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/reference/experimentSpecServer.html b/main/reference/experimentSpecServer.html index d019326e..b524b1dc 100644 --- a/main/reference/experimentSpecServer.html +++ b/main/reference/experimentSpecServer.html @@ -1,7 +1,23 @@ - -Module Server for Experiment Specification — experimentSpecServer • teal.modules.hermes + + + + + + +Module Server for Experiment Specification — experimentSpecServer • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -40,7 +70,8 @@

    Module Server for Experiment Specification

    -

    Usage

    +

    Usage +

    experimentSpecServer(
   id,
   data,
@@ -53,57 +84,73 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    id
    +
    +
    id +

    (string) the shiny module id.

    -
    data
    +
    data +

    (reactive)
    reactive(<teal_data>) holding all the data sets provided during app initialization after going through the filters.

    -
    filter_panel_api
    +
    filter_panel_api +

    (FilterPanelAPI)
    object describing the actual filter panel API.

    -
    mae_name
    +
    mae_name +

    (string)
    name of the MAE data used in the teal module.

    -
    name_annotation
    +
    name_annotation +

    (string or NULL)
    which annotation column to use as name to return in the genes data. If NULL, then the name column will be set to empty strings.

    -
    sample_vars_as_factors
    +
    sample_vars_as_factors +

    (flag)
    whether to convert the sample variables (columns in colData() of the experiment) from character to factor variables.

    -
    with_mae_col_data
    +
    with_mae_col_data +

    (flag)
    whether to include the colData() of the MAE into the experiment colData().

    -
    + +
    -

    Value

    -

    List with the following reactive objects:

    • data: the hermes::AnyHermesData experiment.

      • +

      Value +

      +

      List with the following reactive objects:

      +
        +

      • data: the hermes::AnyHermesData experiment.

      • name: the name of the experiment as selected by the user.

      • genes: a data.frame with the genes in data, with columns id and name.

      • assays: the names of the assays in data.

        • -
    + +
    -

    See also

    +

    See also +

    experimentSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                mae_name) {
   ns <- NS(id)
@@ -185,17 +232,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/function_arguments.html b/main/reference/function_arguments.html index 90523b08..5d0d034f 100644 --- a/main/reference/function_arguments.html +++ b/main/reference/function_arguments.html @@ -1,7 +1,23 @@ - -Standard Function Arguments — function_arguments • teal.modules.hermes + + + + + + +Standard Function Arguments — function_arguments • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -41,50 +71,62 @@

    Standard Function Arguments

    -

    Arguments

    +

    Arguments +

    -
    adtte
    +
    +
    adtte +

    (data frame)
    an adtte dataset.

    -
    usubjid_var
    +
    usubjid_var +

    (string)
    variable name of the subject ID variable.

    -
    mae
    +
    mae +

    (MultiAssayExperiment)
    contains AnyHermesData objects.

    -
    object
    +
    object +

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    -
    genes
    +
    genes +

    (GeneSpec)
    specification for gene(s) (signature), e.g. using hermes::gene_spec().

    -
    experiment_name
    +
    experiment_name +

    (string)
    the desired HermesData to use.

    -
    assay_name
    +
    assay_name +

    (string)
    the assay to define the groups.

    -
    + + - + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/reference/geneSpecInput.html b/main/reference/geneSpecInput.html index ea82f1b5..2de6a0fe 100644 --- a/main/reference/geneSpecInput.html +++ b/main/reference/geneSpecInput.html @@ -1,7 +1,23 @@ - -Module Input for Gene Signature Specification — geneSpecInput • teal.modules.hermes + + + + + + +Module Input for Gene Signature Specification — geneSpecInput • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -40,7 +70,8 @@

    Module Input for Gene Signature Specification

    -

    Usage

    +

    Usage +

    geneSpecInput(
   inputId,
   funs,
@@ -57,63 +88,79 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    inputId
    +
    +
    inputId +

    (string)
    the ID used to call the module input.

    -
    funs
    +
    funs +

    (named list)
    names of this list will be used for the function selection drop down menu.

    -
    label_genes
    +
    label_genes +

    (string)
    label for the gene selection.

    -
    label_funs
    +
    label_funs +

    (string)
    label for the function selection.

    -
    label_text_button
    +
    label_text_button +

    (string)
    label for the text input button.

    -
    label_lock_button
    +
    label_lock_button +

    (string)
    label for the lock button.

    -
    label_select_all_button
    +
    label_select_all_button +

    (string)
    label for the selecting all genes button.

    -
    label_select_none_button
    +
    label_select_none_button +

    (string)
    label for the selecting no genes button.

    -
    max_options
    +
    max_options +

    (count)
    maximum number of gene options rendering and selected via "Select All".

    -
    max_selected
    +
    max_selected +

    (count)
    maximum number of genes which can be selected.

    -
    + +
    -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    geneSpecServer() for the module server and a complete example.

    -

    Examples

    +

    Examples +

    geneSpecInput("my_genes", list(mean = colMeans), label_funs = "Please select function")
 #> <div class="row">
 #>   <div class="col-sm-8">
@@ -179,17 +226,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/geneSpecServer.html b/main/reference/geneSpecServer.html index 3c480d89..e77bfe2a 100644 --- a/main/reference/geneSpecServer.html +++ b/main/reference/geneSpecServer.html @@ -1,7 +1,23 @@ - -Module Server for Gene Signature Specification — geneSpecServer • teal.modules.hermes + + + + + + +Module Server for Gene Signature Specification — geneSpecServer • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -40,7 +70,8 @@

    Module Server for Gene Signature Specification

    -

    Usage

    +

    Usage +

    geneSpecServer(
   id,
   funs,
@@ -52,43 +83,54 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    id
    +
    +
    id +

    (string) the shiny module id.

    -
    funs
    +
    funs +

    (static named list)
    names of this list will be used for the function selection drop down menu.

    -
    gene_choices
    +
    gene_choices +

    (reactive data.frame)
    returns the possible gene choices to populate in the UI, as a data.frame with columns id and name.

    -
    label_modal_title
    +
    label_modal_title +

    (string)
    title for the dialog that asks for the text input.

    - +

    (character)
    lines of text to use for the footer of the dialog.

    -
    + +
    -

    Value

    +

    Value +

    Reactive hermes::GeneSpec which can be used as input for the relevant hermes functions.

    -

    See also

    +

    See also +

    geneSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id, funs) {
   ns <- NS(id)
   teal.widgets::standard_layout(
@@ -158,17 +200,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/h_assign_to_group_list.html b/main/reference/h_assign_to_group_list.html index ed87d2dc..cab2c258 100644 --- a/main/reference/h_assign_to_group_list.html +++ b/main/reference/h_assign_to_group_list.html @@ -1,9 +1,25 @@ - -Helper Function For Group List Creation — h_assign_to_group_list • teal.modules.hermes + + + + + +Helper Function For Group List Creation — h_assign_to_group_list • teal.modules.hermes + + + + + + + +group list."> + + + + Skip to contents @@ -19,11 +35,25 @@ + + +
      +
      • +
    + @@ -43,25 +73,32 @@

    Helper Function For Group List Creation

    -

    Usage

    +

    Usage +

    h_assign_to_group_list(x)
    -

    Arguments

    +

    Arguments +

    -
    x
    +
    +
    x +

    (named list of character)
    input assignment list.

    -
    + +
    -

    Value

    +

    Value +

    A combination list.

    -

    Examples

    +

    Examples +

    assign_list <- list(
   "ASIAN" = "1",
   "BLACK OR AFRICAN AMERICAN" = "1",
@@ -79,17 +116,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/h_collapse_levels.html b/main/reference/h_collapse_levels.html index 43e2b622..598d25ba 100644 --- a/main/reference/h_collapse_levels.html +++ b/main/reference/h_collapse_levels.html @@ -1,11 +1,27 @@ - -Helper Function for Collapsing of Factor Levels — h_collapse_levels • teal.modules.hermes + + + + + +Helper Function for Collapsing of Factor Levels — h_collapse_levels • teal.modules.hermes + + + + + + + +levels are in the order given in the group list."> + + + + Skip to contents @@ -21,11 +37,25 @@ + + +
      +
      • +
    + @@ -46,30 +76,38 @@

    Helper Function for Collapsing of Factor Levels

    -

    Usage

    +

    Usage +

    h_collapse_levels(x, group_list)
    -

    Arguments

    +

    Arguments +

    -
    x
    +
    +
    x +

    (factor)
    original factor.

    -
    group_list
    +
    group_list +

    (named list of character)
    includes the collapsing specification.

    -
    + +
    -

    Value

    +

    Value +

    The transformed factor x with new levels.

    -

    Examples

    +

    Examples +

    set.seed(123)
 x <- factor(sample(
   c("ASIAN", "BLACK OR AFRICAN AMERICAN", "MULTIPLE", "UNKNOWN", "WHITE"),
@@ -86,17 +124,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/h_extract_words.html b/main/reference/h_extract_words.html index dcb8a238..b20d05ec 100644 --- a/main/reference/h_extract_words.html +++ b/main/reference/h_extract_words.html @@ -1,11 +1,27 @@ - -Helper Function to Extract Words — h_extract_words • teal.modules.hermes + + + + + +Helper Function to Extract Words — h_extract_words • teal.modules.hermes + + + + + + + +characters are considered separators."> + + + + Skip to contents @@ -21,11 +37,25 @@ + + +
      +
      • +
    + @@ -46,25 +76,32 @@

    Helper Function to Extract Words

    -

    Usage

    +

    Usage +

    h_extract_words(x)
    -

    Arguments

    +

    Arguments +

    -
    x
    +
    +
    x +

    (string)
    input.

    -
    + +
    -

    Value

    +

    Value +

    Character vector with the extracted words.

    -

    Examples

    +

    Examples +

    h_extract_words("a, b, , c, 234; 34562 - GeneID:bla")
 #> [1] "a"          "b"          "c"          "234"        "34562"     
 #> [6] "GeneID:bla"
@@ -73,17 +110,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/h_gene_data.html b/main/reference/h_gene_data.html index cddd256f..c66c0f75 100644 --- a/main/reference/h_gene_data.html +++ b/main/reference/h_gene_data.html @@ -1,11 +1,27 @@ - -Helper Function to Format Gene Choices — h_gene_data • teal.modules.hermes + + + + + +Helper Function to Format Gene Choices — h_gene_data • teal.modules.hermes + + + + + + + +as a data.frame ready for consumption in h_order_genes() e.g."> + + + + Skip to contents @@ -21,11 +37,25 @@ + + +
      +
      • +
    + @@ -46,38 +76,47 @@

    Helper Function to Format Gene Choices

    -

    Usage

    +

    Usage +

    h_gene_data(object, name_annotation)
    -

    Arguments

    +

    Arguments +

    -
    object
    +
    +
    object +

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    -
    name_annotation
    +
    name_annotation +

    (string or NULL)
    which annotation column to use as name to return in the genes data. If NULL, then the name column will be set to empty strings.

    -
    + +
    -

    Value

    +

    Value +

    A data.frame with id and name columns containing all genes from object.

    -

    Details

    +

    Details +

    Note that missing names or names that only contain whitespace are replaced by empty strings for consistency and better labeling in the UI downstream

    -

    Examples

    +

    Examples +

    object <- hermes::hermes_data[1:10, ]
 h_gene_data(object, "symbol")
 #>                  id         name
@@ -94,17 +133,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/h_km_mae_to_adtte.html b/main/reference/h_km_mae_to_adtte.html index 3e3eaf30..70083c8d 100644 --- a/main/reference/h_km_mae_to_adtte.html +++ b/main/reference/h_km_mae_to_adtte.html @@ -1,7 +1,23 @@ - -Data Preprocessing for ADTTE Module — h_km_mae_to_adtte • teal.modules.hermes + + + + + + +Data Preprocessing for ADTTE Module — h_km_mae_to_adtte • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -40,7 +70,8 @@

    Data Preprocessing for ADTTE Module

    -

    Usage

    +

    Usage +

    h_km_mae_to_adtte(
   adtte,
   mae,
@@ -52,49 +83,61 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    adtte
    +
    +
    adtte +

    (data frame)
    an adtte dataset.

    -
    mae
    +
    mae +

    (MultiAssayExperiment)
    contains AnyHermesData objects.

    -
    genes
    +
    genes +

    (GeneSpec)
    specification for gene(s) (signature), e.g. using hermes::gene_spec().

    -
    experiment_name
    +
    experiment_name +

    (string)
    the desired HermesData to use.

    -
    assay_name
    +
    assay_name +

    (string)
    the assay to define the groups.

    -
    usubjid_var
    +
    usubjid_var +

    (string)
    variable name of the subject ID variable.

    -
    + +
    -

    Value

    +

    Value +

    A data frame containing all columns/rows from adtte that match by subject ID with the row names of the MAE and have the gene samples available in the given experiment. The attribute gene_cols contains the column names for the gene columns.

    -

    Note

    +

    Note +

    The final gene column names can start with a different string than the original gene IDs (or labels), in particular white space and colons are removed.

    -

    Examples

    +

    Examples +

    library(dplyr)
 mae <- hermes::multi_assay_experiment
 adtte <- teal.modules.hermes::rADTTE %>%
@@ -121,17 +164,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/h_order_genes.html b/main/reference/h_order_genes.html index 55f74f94..1070c4f5 100644 --- a/main/reference/h_order_genes.html +++ b/main/reference/h_order_genes.html @@ -1,11 +1,27 @@ - -Helper Function to Order Gene Choices — h_order_genes • teal.modules.hermes + + + + + +Helper Function to Order Gene Choices — h_order_genes • teal.modules.hermes + + + + + + + +all genes with an empty name, ordered by their ID alphabetically."> + + + + Skip to contents @@ -21,11 +37,25 @@ + + +
      +
      • +
    + @@ -46,26 +76,33 @@

    Helper Function to Order Gene Choices

    -

    Usage

    +

    Usage +

    h_order_genes(genes)
    -

    Arguments

    +

    Arguments +

    -
    genes
    +
    +
    genes +

    (data.frame)
    containing id and name columns of the gene choices. Note that no missing values are allowed.

    -
    + +
    -

    Value

    +

    Value +

    The ordered data.frame.

    -

    Examples

    +

    Examples +

    genes <- data.frame(
   id = c("7", "1", "2", "345346", "0"),
   name = c("e", "", "c", "", "a")
@@ -80,17 +117,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/h_parse_genes.html b/main/reference/h_parse_genes.html index 49dacc82..85102c69 100644 --- a/main/reference/h_parse_genes.html +++ b/main/reference/h_parse_genes.html @@ -1,9 +1,25 @@ - -Helper Function to Parse Genes — h_parse_genes • teal.modules.hermes + + + + + +Helper Function to Parse Genes — h_parse_genes • teal.modules.hermes + + + + + + + +with the id and name columns of possible gene choices."> + + + + Skip to contents @@ -19,11 +35,25 @@ + + +
      +
      • +
    + @@ -43,30 +73,38 @@

    Helper Function to Parse Genes

    -

    Usage

    +

    Usage +

    h_parse_genes(words, choices)
    -

    Arguments

    +

    Arguments +

    -
    words
    +
    +
    words +

    (character)
    containing gene IDs or names.

    -
    choices
    +
    choices +

    (data.frame)
    containing id and name columns of the new choices.

    -
    + +
    -

    Value

    +

    Value +

    The subset of choices which matches words in ID or name.

    -

    Examples

    +

    Examples +

    h_parse_genes(
   c("a", "2535"),
   data.frame(id = as.character(2533:2537), name = letters[1:5])
@@ -77,17 +115,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/h_update_gene_selection.html b/main/reference/h_update_gene_selection.html index afe8aca6..69be3b9b 100644 --- a/main/reference/h_update_gene_selection.html +++ b/main/reference/h_update_gene_selection.html @@ -1,11 +1,27 @@ - -Helper Function to Update Gene Selection — h_update_gene_selection • teal.modules.hermes + + + + + +Helper Function to Update Gene Selection — h_update_gene_selection • teal.modules.hermes + + + + + + + +shows a notification if not all selected genes were available."> + + + + Skip to contents @@ -21,11 +37,25 @@ + + +
      +
      • +
    + @@ -46,45 +76,55 @@

    Helper Function to Update Gene Selection

    -

    Usage

    +

    Usage +

    h_update_gene_selection(session, inputId, selected, choices)
    -

    Arguments

    +

    Arguments +

    -
    session
    +
    +
    session +

    (ShinySession)
    the session object.

    -
    inputId
    +
    inputId +

    (string)
    the ID used to call the module input.

    -
    selected
    +
    selected +

    (character)
    currently selected gene IDs.

    -
    choices
    +
    choices +

    (data.frame)
    containing id and name columns of the new choices.

    -
    + + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/reference/heatmap_plot.html b/main/reference/heatmap_plot.html index df4ccb5b..d0bf3055 100644 --- a/main/reference/heatmap_plot.html +++ b/main/reference/heatmap_plot.html @@ -1,7 +1,23 @@ - -Correlation Heatmap Plot — heatmap_plot • teal.modules.hermes + + + + + + +Correlation Heatmap Plot — heatmap_plot • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -40,29 +70,37 @@

    Correlation Heatmap Plot

    -

    Usage

    +

    Usage +

    heatmap_plot(object, assay_name)
    -

    Arguments

    +

    Arguments +

    -
    object
    +
    +
    object +

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    -
    assay_name
    +
    assay_name +

    (string)
    the assay to define the groups.

    -
    + +
    -

    Value

    +

    Value +

    Plot to be displayed in the teal app.

    -

    Examples

    +

    Examples +

    library(hermes)
 #> Loading required package: ggfortify
 #> Loading required package: SummarizedExperiment
@@ -157,17 +195,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/include_css_files.html b/main/reference/include_css_files.html index 53b1b27e..e8faa307 100644 --- a/main/reference/include_css_files.html +++ b/main/reference/include_css_files.html @@ -1,9 +1,25 @@ - -Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.modules.hermes + + + + + +Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.modules.hermes + + + + + + + +as needed. Thus, we do not export this method"> + + + + Skip to contents @@ -19,11 +35,25 @@ + + +
      +
      • +
    + @@ -43,35 +73,43 @@

    Include CSS files from /inst/css/ package director
    -

    Usage

    +

    Usage +

    include_css_files(pattern = "*")
    -

    Arguments

    +

    Arguments +

    -
    pattern
    +
    +
    pattern +

    (character) pattern of files to be included

    -
    + +
    -

    Value

    +

    Value +

    HTML code that includes CSS files

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/reference/include_js_files.html b/main/reference/include_js_files.html index caea14f7..ee534ab1 100644 --- a/main/reference/include_js_files.html +++ b/main/reference/include_js_files.html @@ -1,9 +1,25 @@ - -Include JS files from /inst/js/ package directory to application header — include_js_files • teal.modules.hermes + + + + + +Include JS files from /inst/js/ package directory to application header — include_js_files • teal.modules.hermes + + + + + + + +as needed. Thus, we do not export this method"> + + + + Skip to contents @@ -19,11 +35,25 @@ + + +
      +
      • +
    + @@ -43,39 +73,48 @@

    Include JS files from /inst/js/ package directory
    -

    Usage

    +

    Usage +

    include_js_files(pattern = "*")
    -

    Arguments

    +

    Arguments +

    -
    pattern
    +
    +
    pattern +

    (character) pattern of files to be included, passed to system.file

    -
    except
    +
    except +

    (character) vector of basename filenames to be excluded

    -
    + +
    -

    Value

    +

    Value +

    HTML code that includes JS files

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/reference/index.html b/main/reference/index.html index 35c9aa24..2dc3b9c4 100644 --- a/main/reference/index.html +++ b/main/reference/index.html @@ -1,5 +1,19 @@ - -Package index • teal.modules.hermes + + + + + + +Package index • teal.modules.hermes + + + + + + + + + Skip to contents @@ -15,11 +29,25 @@ + + +
      +
      • +
    + @@ -31,317 +59,414 @@

    Package index

    -

    Package

    +

    Package +

    -
    +
    +
    -
    +
    +
    teal.modules.hermes teal.modules.hermes-package
    -
    teal.modules.hermes Package
    -
    -

    Utility Functions

    +
    +teal.modules.hermes Package
    + +
    +
    +

    Utility Functions +

    -
    +
    +
    -
    +
    +
    h_assign_to_group_list() experimental
    Helper Function For Group List Creation
    -
    +
    +
    +
    h_collapse_levels() experimental
    Helper Function for Collapsing of Factor Levels
    -
    +
    +
    +
    h_extract_words() experimental
    Helper Function to Extract Words
    -
    +
    +
    +
    h_gene_data() experimental
    Helper Function to Format Gene Choices
    -
    +
    +
    +
    h_km_mae_to_adtte() experimental
    Data Preprocessing for ADTTE Module
    -
    +
    +
    +
    h_order_genes() experimental
    Helper Function to Order Gene Choices
    -
    +
    +
    +
    h_parse_genes() experimental
    Helper Function to Parse Genes
    -
    +
    +
    +
    h_update_gene_selection() experimental
    Helper Function to Update Gene Selection
    -
    +
    +
    +
    is_blank() experimental
    Checking for Empty String
    -
    -

    Shiny Modules

    + +
    +
    +

    Shiny Modules +

    -
    +
    +
    -
    +
    +
    adtteSpecInput() experimental
    Module Input for ADTTE Specification
    -
    +
    +
    +
    adtteSpecServer() experimental
    Module Server for ADTTE Specification
    -
    +
    +
    +
    assaySpecInput() experimental
    Module Input for Assay Specification
    -
    +
    +
    +
    assaySpecServer() experimental
    Module Server for Assay Specification
    -
    +
    +
    +
    experimentSpecInput() experimental
    Module Input for Experiment Specification
    -
    +
    +
    +
    experimentSpecServer() experimental
    Module Server for Experiment Specification
    -
    +
    +
    +
    geneSpecInput() experimental
    Module Input for Gene Signature Specification
    -
    +
    +
    +
    geneSpecServer() experimental
    Module Server for Gene Signature Specification
    -
    +
    +
    +
    sampleVarSpecInput() experimental
    Module Input for Sample Variable Specification
    -
    +
    +
    +
    sampleVarSpecServer() experimental
    Module Server for Sample Variable Specification
    -
    +
    +
    +
    multiSampleVarSpecServer() experimental
    Module Server for Specification of Multiple Sample Variables
    -
    -

    Teal Module Functions

    + +
    +
    +

    Teal Module Functions +

    -
    +
    +
    -
    +
    +
    tm_g_barplot() ui_g_barplot() srv_g_barplot() sample_tm_g_barplot() experimental
    Teal Module for RNA-seq Barplot
    -
    +
    +
    +
    tm_g_boxplot() ui_g_boxplot() srv_g_boxplot() sample_tm_g_boxplot() experimental
    Teal Module for RNA-seq Boxplot
    -
    +
    +
    +
    tm_g_forest_tte() ui_g_forest_tte() srv_g_forest_tte() sample_tm_g_forest_tte() experimental
    Teal Module for Survival Forest Plot
    -
    +
    +
    +
    tm_g_km() ui_g_km() srv_g_km() sample_tm_g_km() experimental
    Teal Module for Kaplan-Meier Plot
    -
    +
    +
    +
    tm_g_pca() ui_g_pca() srv_g_pca() sample_tm_g_pca() experimental
    Teal Module for PCA Analysis
    -
    +
    +
    +
    tm_g_quality() ui_g_quality() srv_g_quality() sample_tm_g_quality() experimental
    Teal Module for RNA-seq Quality Control
    -
    +
    +
    +
    tm_g_scatterplot() ui_g_scatterplot() srv_g_scatterplot() sample_tm_g_scatterplot() experimental
    Teal Module for RNA-seq Scatterplot
    -
    +
    +
    +
    tm_g_volcanoplot() ui_g_volcanoplot() srv_g_volcanoplot() sample_tm_g_volcanoplot() experimental
    Teal Module for RNA-seq Volcano Plot
    -
    -

    Graph Functions

    + +
    +
    +

    Graph Functions +

    -
    +
    +
    -
    +
    +
    heatmap_plot() experimental
    Correlation Heatmap Plot
    -
    +
    +
    +
    top_gene_plot() experimental
    Most Expressed Genes Plot
    -
    -

    Assertions

    + +
    +
    +

    Assertions +

    -
    +
    +
    -
    +
    +
    assert_adtte_vars() experimental
    Check for ADTTE Variables
    -
    +
    +
    +
    check_reactive() assert_reactive() test_reactive() experimental
    Check for Reactive Input
    -
    +
    +
    +
    assert_summary_funs() experimental
    Check for List of Summary Functions
    -
    +
    +
    +
    check_tag() assert_tag() test_tag() expect_tag() experimental
    Check for Shiny Tag
    -
    -

    Validations

    + +
    +
    +

    Validations +

    -
    +
    +
    -
    +
    +
    validate_gene_spec() experimental
    Validation of Gene Specification
    -
    +
    +
    +
    validate_n_levels() experimental
    Validation of Number of Levels
    -
    + + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/reference/is_blank.html b/main/reference/is_blank.html index 459f31ca..1bcf89b7 100644 --- a/main/reference/is_blank.html +++ b/main/reference/is_blank.html @@ -1,9 +1,25 @@ - -Checking for Empty String — is_blank • teal.modules.hermes + + + + + +Checking for Empty String — is_blank • teal.modules.hermes + + + + + + + +not yet be initialized from the teal module."> + + + + Skip to contents @@ -19,11 +35,25 @@ + + +
      +
      • +
    + @@ -43,25 +73,32 @@

    Checking for Empty String

    -

    Usage

    +

    Usage +

    is_blank(x)
    -

    Arguments

    +

    Arguments +

    -
    x
    +
    +
    x +

    object to check.

    -
    + +
    -

    Value

    +

    Value +

    Flag whether x is identical to an empty string, i.e. "".

    -

    Examples

    +

    Examples +

    is_blank("")
 #> [1] TRUE
 is_blank(" ")
@@ -69,17 +106,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/module_arguments.html b/main/reference/module_arguments.html index b415e319..193a09e0 100644 --- a/main/reference/module_arguments.html +++ b/main/reference/module_arguments.html @@ -1,7 +1,23 @@ - -Standard Module Arguments — module_arguments • teal.modules.hermes + + + + + + +Standard Module Arguments — module_arguments • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -41,32 +71,42 @@

    Standard Module Arguments

    -

    Arguments

    +

    Arguments +

    -
    data
    +
    +
    data +

    (reactive)
    reactive(<teal_data>) holding all the data sets provided during app initialization after going through the filters.

    -
    label
    +
    label +

    (string)
    menu item label of the module in the teal app.

    -
    inputId
    +
    inputId +

    (string)
    the ID used to call the module input.

    -
    adtte_name
    +
    adtte_name +

    (string)
    name of the ADTTE dataset.

    -
    adtte_vars
    -

    (named list of string)
    -names of the variables to use in the ADTTE dataset. It should comprise elements:

    • aval: the numeric time-to-event variable.

      • +
      adtte_vars +
      +
      +

      (named list of string)
      +names of the variables to use in the ADTTE dataset. It should comprise elements:

      +
        +

      • aval: the numeric time-to-event variable.

      • avalu: the variable holding the unit of aval.

      • is_event: the logical event variable. It needs to be TRUE when there was an observed event, and FALSE if the time is censored without @@ -74,74 +114,89 @@

        Argumentsmae_name +
        mae_name +

        (string)
        name of the MAE data used in the teal module.

        -
        exclude_assays
        +
        exclude_assays +

        (character)
        names of the assays which should not be included in choices in the teal module.

        -
        summary_funs
        +
        summary_funs +

        (named list of functions or NULL)
        functions which can be used in the the gene signatures. For modules that support also multiple genes without summary, NULL can be included to not summarize the genes but provide all of them.

        -
        reporter
        +
        reporter +

        (Reporter) object

        -
        pre_output
        +
        pre_output +

        (shiny.tag or NULL)
        placed before the output to put the output into context (for example a title).

        -
        post_output
        +
        post_output +

        (shiny.tag or NULL)
        placed after the output to put the output into context (for example the shiny::helpText() elements can be useful).

        -
        id
        +
        id +

        (string) the shiny module id.

        -
        plot_height
        +
        plot_height +

        (list)
        list of integers to set the default, minimum, and maximum plot height.

        -
        plot_width
        +
        plot_width +

        (list)
        list of integers to set the default, minimum, and maximum plot width.

        -
        filter_panel_api
        +
        filter_panel_api +

        (FilterPanelAPI)
        object describing the actual filter panel API.

        -
        .test
        +
        .test +

        (flag)
        whether to display the internal structure of the plot for testing purposes.

        -

    + + - + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/reference/multiSampleVarSpecServer.html b/main/reference/multiSampleVarSpecServer.html index 5801b56d..fd513a3c 100644 --- a/main/reference/multiSampleVarSpecServer.html +++ b/main/reference/multiSampleVarSpecServer.html @@ -1,9 +1,25 @@ - -Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer • teal.modules.hermes + + + + + +Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer • teal.modules.hermes + + + + + + + +wrapper makes it much easier to specify in the server function."> + + + + Skip to contents @@ -19,11 +35,25 @@ + + +
      +
      • +
    + @@ -43,42 +73,51 @@

    Module Server for Specification of Multiple Sample Variables

    -

    Usage

    +

    Usage +

    multiSampleVarSpecServer(inputIds, original_data, ...)
    -

    Arguments

    +

    Arguments +

    -
    inputIds
    +
    +
    inputIds +

    (character)
    multiple input IDs corresponding to the different sample variables specified in the UI function.

    -
    original_data
    +
    original_data +

    (reactive SummarizedExperiment)
    input experiment where the sample variables extracted via SummarizedExperiment::colData() should be eligible for selection.

    -
    ...
    +
    ... +

    additional arguments as documented in sampleVarSpecServer(), namely the mandatory experiment_name and the optional categorical_only, num_levels and label_modal_title. transformed_data and assign_lists should not be specified as they are already specified internally here.

    -
    + +
    -

    Value

    +

    Value +

    List with the final transformed experiment_data reactive and a list vars which contains the selected sample variables as reactives under their input ID.

    -

    Examples

    +

    Examples +

    if (FALSE) { # \dontrun{
 # In the server use:
 sample_var_specs <- multiSampleVarSpecServer(
@@ -96,17 +135,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/rADTTE.html b/main/reference/rADTTE.html index 01b17b31..714b381d 100644 --- a/main/reference/rADTTE.html +++ b/main/reference/rADTTE.html @@ -1,5 +1,21 @@ - -Random Time to Event Analysis Dataset — rADTTE • teal.modules.hermes + + + + + + +Random Time to Event Analysis Dataset — rADTTE • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -15,11 +31,25 @@ + + +
      +
      • +
    + @@ -37,31 +67,36 @@

    Random Time to Event Analysis Dataset

    -

    Usage

    +

    Usage +

    rADTTE
    -

    Format

    +

    Format +

    An object of class tbl_df (inherits from tbl, data.frame) with 2000 rows and 67 columns.

    -

    Source

    +

    Source +

    internal

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/reference/sampleVarSpecInput.html b/main/reference/sampleVarSpecInput.html index 26375273..b7641883 100644 --- a/main/reference/sampleVarSpecInput.html +++ b/main/reference/sampleVarSpecInput.html @@ -1,7 +1,23 @@ - -Module Input for Sample Variable Specification — sampleVarSpecInput • teal.modules.hermes + + + + + + +Module Input for Sample Variable Specification — sampleVarSpecInput • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -40,7 +70,8 @@

    Module Input for Sample Variable Specification

    -

    Usage

    +

    Usage +

    sampleVarSpecInput(
   inputId,
   label_vars = "Select sample variable",
@@ -49,33 +80,42 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    inputId
    +
    +
    inputId +

    (string)
    the ID used to call the module input.

    -
    label_vars
    +
    label_vars +

    (string)
    label for the sample variable selection.

    -
    label_levels_button
    +
    label_levels_button +

    (string)
    label for the levels combination button.

    -
    + +
    -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    sampleVarSpecServer() for the module server and a complete example.

    -

    Examples

    +

    Examples +

    sampleVarSpecInput("my_vars", label_vars = "Select faceting variable")
 #> <div class="row">
 #>   <div class="col-sm-8">
@@ -115,17 +155,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/sampleVarSpecServer.html b/main/reference/sampleVarSpecServer.html index 0b3c79dc..6933a5d0 100644 --- a/main/reference/sampleVarSpecServer.html +++ b/main/reference/sampleVarSpecServer.html @@ -1,7 +1,23 @@ - -Module Server for Sample Variable Specification — sampleVarSpecServer • teal.modules.hermes + + + + + + +Module Server for Sample Variable Specification — sampleVarSpecServer • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -40,7 +70,8 @@

    Module Server for Sample Variable Specification

    -

    Usage

    +

    Usage +

    sampleVarSpecServer(
   id,
   experiment_name,
@@ -55,71 +86,87 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    id
    +
    +
    id +

    (string) the shiny module id.

    -
    experiment_name
    +
    experiment_name +

    (reactive string)
    name of the input experiment.

    -
    original_data
    +
    original_data +

    (reactive SummarizedExperiment)
    input experiment where the sample variables extracted via SummarizedExperiment::colData() should be eligible for selection.

    -
    transformed_data
    +
    transformed_data +

    (reactive SummarizedExperiment)
    used when multiple sample variables can be selected in the app. In that case, pass here the pre-transformed data.

    -
    assign_lists
    +
    assign_lists +

    (reactivevalues)
    object to share factor level groupings across multiple sample variables.

    -
    num_levels
    +
    num_levels +

    (count or NULL)
    required number of levels after combining original levels. If NULL then all numbers of levels are allowed.

    -
    categorical_only
    +
    categorical_only +

    (flag)
    whether only categorical variables should be selected from.

    -
    explicit_na
    +
    explicit_na +

    (flag)
    whether the colData of original_data will be transformed with hermes::h_df_factors_with_explicit_na before further processing. That means also that NA will be made an explicit factor level and counted for num_levels.

    -
    label_modal_title
    +
    label_modal_title +

    (string)
    title for the dialog that asks for the text input.

    -
    + +
    -

    Value

    +

    Value +

    Reactive SummarizedExperiment::SummarizedExperiment which can be used as input for the relevant hermes functions.

    -

    Note

    +

    Note +

    Only atomic columns (e.g. not DataFrame columns) of the colData which are not completely missing (NA) will be shown for selection. If num_levels is specified then only factor columns will be available.

    -

    See also

    +

    See also +

    sampleVarSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id) {
   checkmate::assert_class(data, "teal_data")
   ns <- NS(id)
@@ -190,17 +237,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/teal.modules.hermes-package.html b/main/reference/teal.modules.hermes-package.html index 372a23ce..9de51b3c 100644 --- a/main/reference/teal.modules.hermes-package.html +++ b/main/reference/teal.modules.hermes-package.html @@ -1,7 +1,23 @@ - -teal.modules.hermes Package — teal.modules.hermes-package • teal.modules.hermes + + + + + + +teal.modules.hermes Package — teal.modules.hermes-package • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -29,7 +59,8 @@
    -

    teal.modules.hermes Package

    +

    +teal.modules.hermes Package

    Source: R/package.R
    teal.modules.hermes-package.Rd
    @@ -41,16 +72,24 @@

    teal.modules.hermes Package

    -

    See also

    -

    Useful links:

    +
    -

    Author

    +

    Author +

    Maintainer: Dony Unardi unardid@gene.com

    -

    Authors:

    • Daniel Sabanés Bové

      • +

      Authors:

      +
        +

      • Daniel Sabanés Bové

      • Nikolas Burkoff

      • Dinakar Kulkarni

      • Konrad Pagacz

        • @@ -61,26 +100,32 @@

        Author<

      • Stefanie Bienert

      • Haocheng Li

      • Lyndsee Midori Zhang

        • -

      Other contributors:

      • Sorin Voicu [contributor]

        • +
      +

      Other contributors:

      +
        +

      • Sorin Voicu [contributor]

      • Benoit Falquet [contributor]

      • Mahmoud Hallal [contributor]

      • Tim Treis [contributor]

      • Vedha Viyash [contributor]

      • F. Hoffmann-La Roche AG [copyright holder, funder]

        • -
    + +
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/reference/tm_g_barplot.html b/main/reference/tm_g_barplot.html index 36accd87..5ba9d7e9 100644 --- a/main/reference/tm_g_barplot.html +++ b/main/reference/tm_g_barplot.html @@ -1,9 +1,25 @@ - -Teal Module for RNA-seq Barplot — tm_g_barplot • teal.modules.hermes + + + + + +Teal Module for RNA-seq Barplot — tm_g_barplot • teal.modules.hermes + + + + + + + +analysis."> + + + + Skip to contents @@ -19,11 +35,25 @@ + + +
      +
      • +
    + @@ -43,7 +73,8 @@

    Teal Module for RNA-seq Barplot

    -

    Usage

    +

    Usage +

    tm_g_barplot(
   label,
   mae_name,
@@ -79,76 +110,95 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (string)
    menu item label of the module in the teal app.

    -
    mae_name
    +
    mae_name +

    (string)
    name of the MAE data used in the teal module.

    -
    exclude_assays
    +
    exclude_assays +

    (character)
    names of the assays which should not be included in choices in the teal module.

    -
    summary_funs
    +
    summary_funs +

    (named list of functions or NULL)
    functions which can be used in the the gene signatures. For modules that support also multiple genes without summary, NULL can be included to not summarize the genes but provide all of them.

    -
    pre_output
    +
    pre_output +

    (shiny.tag or NULL)
    placed before the output to put the output into context (for example a title).

    -
    post_output
    +
    post_output +

    (shiny.tag or NULL)
    placed after the output to put the output into context (for example the shiny::helpText() elements can be useful).

    -
    .test
    +
    .test +

    (flag)
    whether to display the internal structure of the plot for testing purposes.

    -
    id
    +
    id +

    (string) the shiny module id.

    -
    data
    +
    data +

    (reactive)
    reactive(<teal_data>) holding all the data sets provided during app initialization after going through the filters.

    -
    filter_panel_api
    +
    filter_panel_api +

    (FilterPanelAPI)
    object describing the actual filter panel API.

    -
    reporter
    +
    reporter +

    (Reporter) object

    -
    + +
    -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_barplot(): sets up the user interface.

      • +
        +

      • ui_g_barplot(): sets up the user interface.

      • srv_g_barplot(): sets up the server with reactive graph.

      • sample_tm_g_barplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -171,17 +221,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/tm_g_boxplot.html b/main/reference/tm_g_boxplot.html index aff5f6aa..e0b976ab 100644 --- a/main/reference/tm_g_boxplot.html +++ b/main/reference/tm_g_boxplot.html @@ -1,9 +1,25 @@ - -Teal Module for RNA-seq Boxplot — tm_g_boxplot • teal.modules.hermes + + + + + +Teal Module for RNA-seq Boxplot — tm_g_boxplot • teal.modules.hermes + + + + + + + +analysis."> + + + + Skip to contents @@ -19,11 +35,25 @@ + + +
      +
      • +
    + @@ -43,7 +73,8 @@

    Teal Module for RNA-seq Boxplot

    -

    Usage

    +

    Usage +

    tm_g_boxplot(
   label,
   mae_name,
@@ -79,76 +110,95 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (string)
    menu item label of the module in the teal app.

    -
    mae_name
    +
    mae_name +

    (string)
    name of the MAE data used in the teal module.

    -
    exclude_assays
    +
    exclude_assays +

    (character)
    names of the assays which should not be included in choices in the teal module.

    -
    summary_funs
    +
    summary_funs +

    (named list of functions or NULL)
    functions which can be used in the the gene signatures. For modules that support also multiple genes without summary, NULL can be included to not summarize the genes but provide all of them.

    -
    pre_output
    +
    pre_output +

    (shiny.tag or NULL)
    placed before the output to put the output into context (for example a title).

    -
    post_output
    +
    post_output +

    (shiny.tag or NULL)
    placed after the output to put the output into context (for example the shiny::helpText() elements can be useful).

    -
    .test
    +
    .test +

    (flag)
    whether to display the internal structure of the plot for testing purposes.

    -
    id
    +
    id +

    (string) the shiny module id.

    -
    data
    +
    data +

    (reactive)
    reactive(<teal_data>) holding all the data sets provided during app initialization after going through the filters.

    -
    filter_panel_api
    +
    filter_panel_api +

    (FilterPanelAPI)
    object describing the actual filter panel API.

    -
    reporter
    +
    reporter +

    (Reporter) object

    -
    + +
    -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_boxplot(): sets up the user interface.

      • +
        +

      • ui_g_boxplot(): sets up the user interface.

      • srv_g_boxplot(): sets up the server with reactive graph.

      • sample_tm_g_boxplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -171,17 +221,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/tm_g_forest_tte.html b/main/reference/tm_g_forest_tte.html index a243375f..39bc4471 100644 --- a/main/reference/tm_g_forest_tte.html +++ b/main/reference/tm_g_forest_tte.html @@ -1,7 +1,23 @@ - -Teal Module for Survival Forest Plot — tm_g_forest_tte • teal.modules.hermes + + + + + + +Teal Module for Survival Forest Plot — tm_g_forest_tte • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -40,7 +70,8 @@

    Teal Module for Survival Forest Plot

    -

    Usage

    +

    Usage +

    tm_g_forest_tte(
   label,
   adtte_name,
@@ -86,27 +117,36 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (string)
    menu item label of the module in the teal app.

    -
    adtte_name
    +
    adtte_name +

    (string)
    name of the ADTTE dataset.

    -
    mae_name
    +
    mae_name +

    (string)
    name of the MAE data used in the teal module.

    -
    adtte_vars
    -

    (named list of string)
    -names of the variables to use in the ADTTE dataset. It should comprise elements:

    • aval: the numeric time-to-event variable.

      • +
      adtte_vars +
      +
      +

      (named list of string)
      +names of the variables to use in the ADTTE dataset. It should comprise elements:

      +
        +

      • aval: the numeric time-to-event variable.

      • avalu: the variable holding the unit of aval.

      • is_event: the logical event variable. It needs to be TRUE when there was an observed event, and FALSE if the time is censored without @@ -114,76 +154,94 @@

        Argumentsexclude_assays +
        exclude_assays +

        (character)
        names of the assays which should not be included in choices in the teal module.

        -
        summary_funs
        +
        summary_funs +

        (named list of functions or NULL)
        functions which can be used in the the gene signatures. For modules that support also multiple genes without summary, NULL can be included to not summarize the genes but provide all of them.

        -
        pre_output
        +
        pre_output +

        (shiny.tag or NULL)
        placed before the output to put the output into context (for example a title).

        -
        post_output
        +
        post_output +

        (shiny.tag or NULL)
        placed after the output to put the output into context (for example the shiny::helpText() elements can be useful).

        -
        plot_height
        +
        plot_height +

        (list)
        list of integers to set the default, minimum, and maximum plot height.

        -
        plot_width
        +
        plot_width +

        (list)
        list of integers to set the default, minimum, and maximum plot width.

        -
        .test
        +
        .test +

        (flag)
        whether to display the internal structure of the plot for testing purposes.

        -
        id
        +
        id +

        (string) the shiny module id.

        -
        data
        +
        data +

        (reactive)
        reactive(<teal_data>) holding all the data sets provided during app initialization after going through the filters.

        -
        filter_panel_api
        +
        filter_panel_api +

        (FilterPanelAPI)
        object describing the actual filter panel API.

        -
        reporter
        +
        reporter +

        (Reporter) object

        -

    + +
    -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_forest_tte(): sets up the user interface.

      • +
        +

      • ui_g_forest_tte(): sets up the user interface.

      • srv_g_forest_tte(): sets up the server with reactive graph.

      • sample_tm_g_forest_tte(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    library(dplyr)
 
 data <- teal_data()
@@ -218,17 +276,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/tm_g_km.html b/main/reference/tm_g_km.html index 528099c7..743af770 100644 --- a/main/reference/tm_g_km.html +++ b/main/reference/tm_g_km.html @@ -1,9 +1,25 @@ - -Teal Module for Kaplan-Meier Plot — tm_g_km • teal.modules.hermes + + + + + +Teal Module for Kaplan-Meier Plot — tm_g_km • teal.modules.hermes + + + + + + + +ADaM structure."> + + + + Skip to contents @@ -19,11 +35,25 @@ + + +
      +
      • +
    + @@ -43,7 +73,8 @@

    Teal Module for Kaplan-Meier Plot

    -

    Usage

    +

    Usage +

    tm_g_km(
   label,
   adtte_name,
@@ -85,27 +116,36 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (string)
    menu item label of the module in the teal app.

    -
    adtte_name
    +
    adtte_name +

    (string)
    name of the ADTTE dataset.

    -
    mae_name
    +
    mae_name +

    (string)
    name of the MAE data used in the teal module.

    -
    adtte_vars
    -

    (named list of string)
    -names of the variables to use in the ADTTE dataset. It should comprise elements:

    • aval: the numeric time-to-event variable.

      • +
      adtte_vars +
      +
      +

      (named list of string)
      +names of the variables to use in the ADTTE dataset. It should comprise elements:

      +
        +

      • aval: the numeric time-to-event variable.

      • avalu: the variable holding the unit of aval.

      • is_event: the logical event variable. It needs to be TRUE when there was an observed event, and FALSE if the time is censored without @@ -113,66 +153,82 @@

        Argumentsexclude_assays +
        exclude_assays +

        (character)
        names of the assays which should not be included in choices in the teal module.

        -
        summary_funs
        +
        summary_funs +

        (named list of functions or NULL)
        functions which can be used in the the gene signatures. For modules that support also multiple genes without summary, NULL can be included to not summarize the genes but provide all of them.

        -
        pre_output
        +
        pre_output +

        (shiny.tag or NULL)
        placed before the output to put the output into context (for example a title).

        -
        post_output
        +
        post_output +

        (shiny.tag or NULL)
        placed after the output to put the output into context (for example the shiny::helpText() elements can be useful).

        -
        .test
        +
        .test +

        (flag)
        whether to display the internal structure of the plot for testing purposes.

        -
        id
        +
        id +

        (string) the shiny module id.

        -
        data
        +
        data +

        (reactive)
        reactive(<teal_data>) holding all the data sets provided during app initialization after going through the filters.

        -
        filter_panel_api
        +
        filter_panel_api +

        (FilterPanelAPI)
        object describing the actual filter panel API.

        -
        reporter
        +
        reporter +

        (Reporter) object

        -

    + +
    -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_km(): sets up the user interface.

      • +
        +

      • ui_g_km(): sets up the user interface.

      • srv_g_km(): sets up the user interface.

      • sample_tm_g_km(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    library(dplyr)
 
 data <- teal_data()
@@ -211,17 +267,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/tm_g_pca.html b/main/reference/tm_g_pca.html index 0f70736d..37ee2bd0 100644 --- a/main/reference/tm_g_pca.html +++ b/main/reference/tm_g_pca.html @@ -1,11 +1,27 @@ - -Teal Module for PCA Analysis — tm_g_pca • teal.modules.hermes + + + + + +Teal Module for PCA Analysis — tm_g_pca • teal.modules.hermes + + + + + + + +variables."> + + + + Skip to contents @@ -21,11 +37,25 @@ + + +
      +
      • +
    + @@ -46,7 +76,8 @@

    Teal Module for PCA Analysis

    -

    Usage

    +

    Usage +

    tm_g_pca(
   label,
   mae_name,
@@ -72,70 +103,88 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (string)
    menu item label of the module in the teal app.

    -
    mae_name
    +
    mae_name +

    (string)
    name of the MAE data used in the teal module.

    -
    exclude_assays
    +
    exclude_assays +

    (character)
    names of the assays which should not be included in choices in the teal module.

    -
    pre_output
    +
    pre_output +

    (shiny.tag or NULL)
    placed before the output to put the output into context (for example a title).

    -
    post_output
    +
    post_output +

    (shiny.tag or NULL)
    placed after the output to put the output into context (for example the shiny::helpText() elements can be useful).

    -
    .test
    +
    .test +

    (flag)
    whether to display the internal structure of the plot for testing purposes.

    -
    id
    +
    id +

    (string) the shiny module id.

    -
    data
    +
    data +

    (reactive)
    reactive(<teal_data>) holding all the data sets provided during app initialization after going through the filters.

    -
    filter_panel_api
    +
    filter_panel_api +

    (FilterPanelAPI)
    object describing the actual filter panel API.

    -
    reporter
    +
    reporter +

    (Reporter) object

    -
    + +
    -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_pca(): sets up the user interface.

      • +
        +

      • ui_g_pca(): sets up the user interface.

      • srv_g_pca(): sets up the server with reactive graph.

      • sample_tm_g_pca(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -158,17 +207,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/tm_g_quality.html b/main/reference/tm_g_quality.html index 4a14330a..3609e571 100644 --- a/main/reference/tm_g_quality.html +++ b/main/reference/tm_g_quality.html @@ -1,11 +1,27 @@ - -Teal Module for RNA-seq Quality Control — tm_g_quality • teal.modules.hermes + + + + + +Teal Module for RNA-seq Quality Control — tm_g_quality • teal.modules.hermes + + + + + + + +for RNA-seq gene expression quality control."> + + + + Skip to contents @@ -21,11 +37,25 @@ + + +
      +
      • +
    + @@ -46,7 +76,8 @@

    Teal Module for RNA-seq Quality Control

    -

    Usage

    +

    Usage +

    tm_g_quality(
   label,
   mae_name,
@@ -72,70 +103,88 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (string)
    menu item label of the module in the teal app.

    -
    mae_name
    +
    mae_name +

    (string)
    name of the MAE data used in the teal module.

    -
    exclude_assays
    +
    exclude_assays +

    (character)
    names of the assays which should not be included in choices in the teal module.

    -
    pre_output
    +
    pre_output +

    (shiny.tag or NULL)
    placed before the output to put the output into context (for example a title).

    -
    post_output
    +
    post_output +

    (shiny.tag or NULL)
    placed after the output to put the output into context (for example the shiny::helpText() elements can be useful).

    -
    .test
    +
    .test +

    (flag)
    whether to display the internal structure of the plot for testing purposes.

    -
    id
    +
    id +

    (string) the shiny module id.

    -
    data
    +
    data +

    (reactive)
    reactive(<teal_data>) holding all the data sets provided during app initialization after going through the filters.

    -
    filter_panel_api
    +
    filter_panel_api +

    (FilterPanelAPI)
    object describing the actual filter panel API.

    -
    reporter
    +
    reporter +

    (Reporter) object

    -
    + +
    -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_quality(): sets up the user interface.

      • +
        +

      • ui_g_quality(): sets up the user interface.

      • srv_g_quality(): sets up the server with reactive graphs.

      • sample_tm_g_quality(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -157,17 +206,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/tm_g_scatterplot.html b/main/reference/tm_g_scatterplot.html index 5d9e7b48..747cec46 100644 --- a/main/reference/tm_g_scatterplot.html +++ b/main/reference/tm_g_scatterplot.html @@ -1,9 +1,25 @@ - -Teal Module for RNA-seq Scatterplot — tm_g_scatterplot • teal.modules.hermes + + + + + +Teal Module for RNA-seq Scatterplot — tm_g_scatterplot • teal.modules.hermes + + + + + + + +analysis."> + + + + Skip to contents @@ -19,11 +35,25 @@ + + +
      +
      • +
    + @@ -43,7 +73,8 @@

    Teal Module for RNA-seq Scatterplot

    -

    Usage

    +

    Usage +

    tm_g_scatterplot(
   label,
   mae_name,
@@ -79,76 +110,95 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (string)
    menu item label of the module in the teal app.

    -
    mae_name
    +
    mae_name +

    (string)
    name of the MAE data used in the teal module.

    -
    exclude_assays
    +
    exclude_assays +

    (character)
    names of the assays which should not be included in choices in the teal module.

    -
    summary_funs
    +
    summary_funs +

    (named list of functions or NULL)
    functions which can be used in the the gene signatures. For modules that support also multiple genes without summary, NULL can be included to not summarize the genes but provide all of them.

    -
    pre_output
    +
    pre_output +

    (shiny.tag or NULL)
    placed before the output to put the output into context (for example a title).

    -
    post_output
    +
    post_output +

    (shiny.tag or NULL)
    placed after the output to put the output into context (for example the shiny::helpText() elements can be useful).

    -
    .test
    +
    .test +

    (flag)
    whether to display the internal structure of the plot for testing purposes.

    -
    id
    +
    id +

    (string) the shiny module id.

    -
    data
    +
    data +

    (reactive)
    reactive(<teal_data>) holding all the data sets provided during app initialization after going through the filters.

    -
    filter_panel_api
    +
    filter_panel_api +

    (FilterPanelAPI)
    object describing the actual filter panel API.

    -
    reporter
    +
    reporter +

    (Reporter) object

    -
    + +
    -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_scatterplot(): sets up the user interface.

      • +
        +

      • ui_g_scatterplot(): sets up the user interface.

      • srv_g_scatterplot(): sets up the server with reactive graph.

      • sample_tm_g_scatterplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -171,17 +221,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/tm_g_volcanoplot.html b/main/reference/tm_g_volcanoplot.html index 00854da2..fcba1f67 100644 --- a/main/reference/tm_g_volcanoplot.html +++ b/main/reference/tm_g_volcanoplot.html @@ -1,9 +1,25 @@ - -Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot • teal.modules.hermes + + + + + +Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot • teal.modules.hermes + + + + + + + +analysis."> + + + + Skip to contents @@ -19,11 +35,25 @@ + + +
      +
      • +
    + @@ -43,7 +73,8 @@

    Teal Module for RNA-seq Volcano Plot

    -

    Usage

    +

    Usage +

    tm_g_volcanoplot(
   label,
   mae_name,
@@ -69,70 +100,88 @@ 
    Usage
    -

    Arguments

    +

    Arguments +

    -
    label
    +
    +
    label +

    (string)
    menu item label of the module in the teal app.

    -
    mae_name
    +
    mae_name +

    (string)
    name of the MAE data used in the teal module.

    -
    exclude_assays
    +
    exclude_assays +

    (character)
    names of the assays which should not be included in choices in the teal module.

    -
    pre_output
    +
    pre_output +

    (shiny.tag or NULL)
    placed before the output to put the output into context (for example a title).

    -
    post_output
    +
    post_output +

    (shiny.tag or NULL)
    placed after the output to put the output into context (for example the shiny::helpText() elements can be useful).

    -
    .test
    +
    .test +

    (flag)
    whether to display the internal structure of the plot for testing purposes.

    -
    id
    +
    id +

    (string) the shiny module id.

    -
    data
    +
    data +

    (reactive)
    reactive(<teal_data>) holding all the data sets provided during app initialization after going through the filters.

    -
    filter_panel_api
    +
    filter_panel_api +

    (FilterPanelAPI)
    object describing the actual filter panel API.

    -
    reporter
    +
    reporter +

    (Reporter) object

    -
    + +
    -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_volcanoplot(): sets up the user interface.

      • +
        +

      • ui_g_volcanoplot(): sets up the user interface.

      • srv_g_volcanoplot(): sets up the server with reactive graph.

      • sample_tm_g_volcanoplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -155,17 +204,19 @@ 
    Examples
    + +
    - + + - + + diff --git a/main/reference/top_gene_plot.html b/main/reference/top_gene_plot.html index dc5b285c..a48cd2bb 100644 --- a/main/reference/top_gene_plot.html +++ b/main/reference/top_gene_plot.html @@ -1,7 +1,23 @@ - -Most Expressed Genes Plot — top_gene_plot • teal.modules.hermes + + + + + + +Most Expressed Genes Plot — top_gene_plot • teal.modules.hermes + + + + + + + + + + + Skip to contents @@ -17,11 +33,25 @@ + + +
      +
      • +
    + @@ -40,46 +70,56 @@

    Most Expressed Genes Plot

    -

    Usage

    +

    Usage +

    top_gene_plot(object, assay_name)
    -

    Arguments

    +

    Arguments +

    -
    object
    +
    +
    object +

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    -
    assay_name
    +
    assay_name +

    (string)
    the assay to define the groups.

    -
    + +
    -

    Value

    +

    Value +

    Plot to be displayed in the teal app.

    -

    Examples

    +

    Examples +

    library(hermes)
 object <- HermesData(summarized_experiment)
 result <- top_gene_plot(object, assay_name = "counts")
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/reference/validate_gene_spec.html b/main/reference/validate_gene_spec.html index d943afed..6d73d240 100644 --- a/main/reference/validate_gene_spec.html +++ b/main/reference/validate_gene_spec.html @@ -1,9 +1,25 @@ - -Validation of Gene Specification — validate_gene_spec • teal.modules.hermes + + + + + +Validation of Gene Specification — validate_gene_spec • teal.modules.hermes + + + + + + + +one gene selected and that all genes are included in possible choices."> + + + + Skip to contents @@ -19,11 +35,25 @@ + + +
      +
      • +
    + @@ -43,35 +73,43 @@

    Validation of Gene Specification

    -

    Usage

    +

    Usage +

    validate_gene_spec(gene_spec, gene_choices)
    -

    Arguments

    +

    Arguments +

    -
    gene_spec
    +
    +
    gene_spec +

    (GeneSpec)
    gene specification.

    -
    gene_choices
    +
    gene_choices +

    (character)
    all possible gene choices.

    -
    + + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/reference/validate_n_levels.html b/main/reference/validate_n_levels.html index fda60cfe..12adb4eb 100644 --- a/main/reference/validate_n_levels.html +++ b/main/reference/validate_n_levels.html @@ -1,9 +1,25 @@ - -Validation of Number of Levels — validate_n_levels • teal.modules.hermes + + + + + +Validation of Number of Levels — validate_n_levels • teal.modules.hermes + + + + + + + +the specified number of levels."> + + + + Skip to contents @@ -19,11 +35,25 @@ + + +
      +
      • +
    + @@ -43,39 +73,48 @@

    Validation of Number of Levels

    -

    Usage

    +

    Usage +

    validate_n_levels(x, name, n_levels)
    -

    Arguments

    +

    Arguments +

    -
    x
    +
    +
    x +

    (factor)
    factor to validate.

    -
    name
    +
    name +

    (string)
    name of x in the app.

    -
    n_levels
    +
    n_levels +

    (count)
    required number of factor levels in x.

    -
    + + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    - + + - + + diff --git a/main/search.json b/main/search.json index 333aa7f6..240d394b 100644 --- a/main/search.json +++ b/main/search.json @@ -1 +1 @@ -[{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contribution Guidelines","title":"Contribution Guidelines","text":"🙏 Thank taking time contribute! input deeply valued, whether issue, pull request, even feedback, regardless size, content scope.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 📔 Code Conduct 🗃 License 📜 Issues 🚩 Pull requests 💻 Coding guidelines 🏆 Recognition model ❓ Questions","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Contribution Guidelines","text":"Please refer project documentation brief introduction. Please also see articles within project documentation additional information.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"Code Conduct governs project. Participants contributors expected follow rules outlined therein.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"contributions covered project’s license.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests, bugs. submitting new issue, please check issue already reported. issue already exists, please upvote existing issue 👍. new feature requests, please elaborate context benefit feature users, developers, relevant personas.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"Pull requests","what":"GitHub Flow","title":"Contribution Guidelines","text":"repository uses GitHub Flow model collaboration. submit pull request: Create branch Please see branch naming convention . don’t write access repository, please fork . Make changes Make sure code passes checks imposed GitHub Actions well documented well tested unit tests sufficiently covering changes introduced Create pull request (PR) pull request description, please link relevant issue (), provide detailed description change, include assumptions. Address review comments, Post approval Merge PR write access. Otherwise, reviewer merge PR behalf. Pat back Congratulations! 🎉 now official contributor project! grateful contribution.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"branch-naming-convention","dir":"","previous_headings":"Pull requests","what":"Branch naming convention","title":"Contribution Guidelines","text":"Suppose changes related current issue current project; please name branch follows: _. Please use underscore (_) delimiter word separation. example, 420_fix_ui_bug suitable branch name change resolving UI-related bug reported issue number 420 current project. change affects multiple repositories, please name branches follows: __. example, 69_awesomeproject_fix_spelling_error reference issue 69 reported project awesomeproject aims resolve one spelling errors multiple (likely related) repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"Pull requests","what":"monorepo and staged.dependencies","title":"Contribution Guidelines","text":"Sometimes might need change upstream dependent package(s) able submit meaningful change. using staged.dependencies functionality simulate monorepo behavior. dependency configuration already specified project’s staged_dependencies.yaml file. need name feature branches appropriately. exception branch naming convention described . Please refer staged.dependencies package documentation details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"coding-guidelines","dir":"","previous_headings":"","what":"Coding guidelines","title":"Contribution Guidelines","text":"repository follows unified processes standards adopted maintainers ensure software development carried consistently within teams cohesively across repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"Coding guidelines","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide uses lintr lint checks. Customized lint configurations available repository’s .lintr file.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"dependency-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency management","title":"Contribution Guidelines","text":"Lightweight right weight. repository follows tinyverse recommedations limiting dependencies minimum.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"dependency-version-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency version management","title":"Contribution Guidelines","text":"code compatible (!) historical versions given dependenct package, required specify minimal version DESCRIPTION file. particular: development version requires (imports) development version another package - required put abc (>= 1.2.3.9000).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version along recent dependencies CRAN BioConductor. recommend working environment also set way. can find details R version packages used R CMD check GitHub Action execution log - step prints R sessionInfo(). discover bugs older R versions older set dependencies, please create relevant bug reports.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend use pre-commit tool combined R hooks pre-commit execute checks committing pushing changes. Pre-commit hooks already available repository’s .pre-commit-config.yaml file.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"mentioned previously, contributions deeply valued appreciated. contribution data available part repository insights, recognize significant contribution hence add contributor package authors list, following rules enforced: Minimum 5% lines code authored* (determined git blame query) top 5 contributors terms number commits lines added lines removed* *Excluding auto-generated code, including limited roxygen comments renv.lock files. package maintainer also reserves right adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"questions","dir":"","previous_headings":"","what":"Questions","title":"Contribution Guidelines","text":"questions regarding contribution guidelines, please contact package/repository maintainer.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/SECURITY.html","id":"reporting-security-issues","dir":"","previous_headings":"","what":"Reporting Security Issues","title":"Security Policy","text":"believe found security vulnerability repositories organization, please report us coordinated disclosure. Please report security vulnerabilities public GitHub issues, discussions, pull requests. Instead, please send email vulnerability.management[@]roche.com. Please include much information listed can help us better understand resolve issue: type issue (e.g., buffer overflow, SQL injection, cross-site scripting) Full paths source file(s) related manifestation issue location affected source code (tag/branch/commit direct URL) special configuration required reproduce issue Step--step instructions reproduce issue Proof--concept exploit code (possible) Impact issue, including attacker might exploit issue information help us triage report quickly.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/SECURITY.html","id":"data-security-standards-dss","dir":"","previous_headings":"","what":"Data Security Standards (DSS)","title":"Security Policy","text":"Please make sure reporting issues form bug, feature, pull request, sensitive information PII, PHI, PCI completely removed text attachments, including pictures videos.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Getting Started","text":"teal.modules.hermes package implementing number teal modules exploration RNA-sequencing counts data. addition predefined modules, teal.modules.hermes enables quick easy ad-hoc module creation.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"ad-hoc-module-example","dir":"Articles","previous_headings":"","what":"Ad-hoc module example","title":"Getting Started","text":"Let’s assume function awesome_plot() takes count matrix makes awesome plot . Now like make Shiny app can filter patients, samples, select experiment MultiAssayExperiment (MAE), select count matrix experiment, etc. Nothing easier teal.modules.hermes! show quickly spin UI, server put together nice little app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"ui-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"UI function","title":"Getting Started","text":"teal.modules.hermes provide modules make experiment assay selection super easy, see UI part:","code":"ui <- function(id, mae_name) { ns <- NS(id) teal.widgets::standard_layout( encoding = uiOutput(ns(\"encoding_ui\")), output = plotOutput(ns(\"awesome_plot\")) ) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"server-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"Server function","title":"Getting Started","text":"Similarly server use modules, call awesome plotting function.","code":"srv <- function(input, output, session, data, filter_panel_api, mae_name) { output$encoding_ui <- renderUI({ tags$div( experimentSpecInput(session$ns(\"experiment\"), data, mae_name), assaySpecInput(session$ns(\"assay\")) ) }) experiment <- experimentSpecServer( \"experiment\", data = data, filter_panel_api = filter_panel_api, mae_name = mae_name, name_annotation = NULL # If you have a gene name column in your rowData, can specify here. ) assay <- assaySpecServer(\"assay\", experiment$assays) output$awesome_plot <- renderPlot({ data <- experiment$data() assay <- assay() req(assay %in% SummarizedExperiment::assayNames(data)) counts <- SummarizedExperiment::assay(data, assay) df <- data.frame(gene = rownames(counts), counts = rowSums(counts)) df <- na.omit(df[order(df$counts, decreasing = TRUE), ]) df$gene <- factor(df$gene, levels = df$gene) df <- df[1:10, ] ggplot(df, aes(x = gene, y = counts)) + geom_col() + theme(axis.text.x = element_text(angle = 90)) }) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"app-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"App function","title":"Getting Started","text":"Now let’s assume want spin app MAE.","code":"awesome_app <- function(mae, label = \"My awesome app\") { mae_name <- \"MAE\" data <- teal_data(MAE = hermes::lapply(mae, hermes::HermesData)) app <- init( data = data, modules = teal::modules( module( label = label, server = srv, server_args = list(mae_name = mae_name), ui = ui, ui_args = list(mae_name = mae_name), datanames = mae_name ) ) ) shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"testing-it","dir":"Articles","previous_headings":"Ad-hoc module example","what":"Testing it","title":"Getting Started","text":"test :","code":"awesome_app(hermes::multi_assay_experiment)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Dony Unardi. Maintainer. Daniel Sabanés Bové. Author. Nikolas Burkoff. Author. Dinakar Kulkarni. Author. Konrad Pagacz. Author. Namrata Bhatia. Author. Dawid Kaledkowski. Author. Pawel Rucki. Author. Jeff Luong. Author. Stefanie Bienert. Author. Haocheng Li. Author. Lyndsee Midori Zhang. Author. Sorin Voicu. Contributor. Benoit Falquet. Contributor. Mahmoud Hallal. Contributor. Tim Treis. Contributor. Vedha Viyash. Contributor. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Sabanés Bové D, Burkoff N, Kulkarni D, Pagacz K, Bhatia N, Kaledkowski D, Rucki P, Luong J, Bienert S, Li H, Zhang L (2024). teal.modules.hermes: RNA-Seq Analysis Modules Add Teal Application. R package version 0.1.6.9024, https://github.com/insightsengineering/teal.modules.hermes/, https://insightsengineering.github.io/teal.modules.hermes/.","code":"@Manual{, title = {teal.modules.hermes: RNA-Seq Analysis Modules to Add to a Teal Application}, author = {Daniel {Sabanés Bové} and Nikolas Burkoff and Dinakar Kulkarni and Konrad Pagacz and Namrata Bhatia and Dawid Kaledkowski and Pawel Rucki and Jeff Luong and Stefanie Bienert and Haocheng Li and Lyndsee Midori Zhang}, year = {2024}, note = {R package version 0.1.6.9024, https://github.com/insightsengineering/teal.modules.hermes/}, url = {https://insightsengineering.github.io/teal.modules.hermes/}, }"},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/index.html","id":"what-is-teal","dir":"","previous_headings":"What is what","what":"What is teal?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"teal shiny-based interactive exploration framework analyzing clinical trials data. teal currently provides dynamic filtering facility diverse data viewers. teal shiny applications built using standard shiny modules. See teal page details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/index.html","id":"what-is-hermes","dir":"","previous_headings":"What is what","what":"What is hermes?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"hermes facilitates preprocessing, analyzing, reporting RNA-seq data. core functionality built BioConductor ecosystem, especially SummarizedExperiment class HermesData class inherits. See vignette details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/index.html","id":"so-what-is-then-tealmoduleshermes","dir":"","previous_headings":"What is what","what":"So what is then teal.modules.hermes?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"teal.modules.hermes provides teal modules (can used part teal app), interactive RNA-seq data analysis using hermes. heavily built BioConductor classes, particular MultiAssayExperiment (MAE) expected contain HermesData experiments.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"See package vignettes browseVignettes(package = \"teal.modules.hermes\") usage package.","code":"# stable versions # install.packages(\"pak\") pak::pkg_install(\"insightsengineering/teal.modules.hermes@*release\") # beta versions # install.packages(\"pak\") pak::pkg_install(\"insightsengineering/teal.modules.hermes\")"},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for ADTTE Specification — adtteSpecInput","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"defines input ADTTE specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"","code":"adtteSpecInput(inputId, label_paramcd = \"Select Endpoint\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"inputId (string) ID used call module input. label_paramcd (string) label endpoint (PARAMCD) selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for ADTTE Specification — adtteSpecServer","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"defines server part ADTTE specification. resulting data set binned_adtte_subset contains subset ADTTE selected time--event endpoint, joined together gene information extracted specified assay experiment, numeric factor columns. factor column created binning numeric column according quantile cutoffs specified probs.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"","code":"adtteSpecServer( id, data, mae_name, adtte_name, adtte_vars, experiment_data, experiment_name, assay, genes, probs )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"id (string) shiny module id. data (reactive)reactive() holding data sets provided app initialization going filters. mae_name (string) name MAE data used teal module. adtte_name (string) name ADTTE dataset. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. experiment_data (reactive AnyHermesData) input experiment. experiment_name (reactive string) name input experiment. assay (reactive string) name assay. genes (reactive GeneSpec) gene specification. probs (reactive numeric) probabilities bin gene gene signature .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"List following elements: binned_adtte_subset: reactive containing joined ADTTE gene data. gene_col: reactive containing string column name original numeric gene variable. gene_factor: string variable name binned gene data. time_unit: reactive string time unit current subset.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"","code":"library(dplyr) #> #> Attaching package: ‘dplyr’ #> The following object is masked from ‘package:testthat’: #> #> matches #> The following objects are masked from ‘package:stats’: #> #> filter, lag #> The following objects are masked from ‘package:base’: #> #> intersect, setdiff, setequal, union ui <- function(id) { ns <- NS(id) teal.widgets::standard_layout( encoding = uiOutput(ns(\"encoding_ui\")), output = verbatimTextOutput(ns(\"summary\")) ) } server <- function(id, data, filter_panel_api) { checkmate::assert_class(data, \"reactive\") checkmate::assert_class(shiny::isolate(data()), \"teal_data\") moduleServer(id, function(input, output, session) { output$encoding_ui <- renderUI({ tags$div( experimentSpecInput(session$ns(\"experiment\"), data, mae_name = \"MAE\"), assaySpecInput(session$ns(\"assay\")), geneSpecInput(session$ns(\"genes\"), funs = list(Mean = colMeans)), adtteSpecInput(session$ns(\"adtte\")) ) }) experiment <- experimentSpecServer( \"experiment\", data = data, filter_panel_api = filter_panel_api, mae_name = \"MAE\" ) assay <- assaySpecServer( \"assay\", assays = experiment$assays ) genes <- geneSpecServer( \"genes\", funs = list(Mean = colMeans), gene_choices = experiment$genes ) adtte <- adtteSpecServer( \"adtte\", data = data, adtte_name = \"ADTTE\", mae_name = \"MAE\", adtte_vars = list( aval = \"AVAL\", avalu = \"AVALU\", is_event = \"is_event\", paramcd = \"PARAMCD\", usubjid = \"USUBJID\" ), experiment_data = experiment$data, experiment_name = experiment$name, assay = assay, genes = genes, probs = reactive({ 0.5 }) ) output$summary <- renderPrint({ binned_adtte_subset <- adtte$binned_adtte_subset() summary(binned_adtte_subset) }) }) } my_app <- function() { data <- teal_data() data <- within(data, { ADSL <- teal.data::rADSL ADTTE <- teal.modules.hermes::rADTTE %>% dplyr::mutate(is_event = .data$CNSR == 0) MAE <- hermes::multi_assay_experiment }) datanames <- c(\"ADSL\", \"ADTTE\", \"MAE\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames] app <- init( data = data, modules = modules( module( label = \"adtteSpec example\", server = server, ui = ui, datanames = \"all\" ) ) ) shinyApp(app$ui, app$server) } if (interactive()) { my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Assay Specification — assaySpecInput","title":"Module Input for Assay Specification — assaySpecInput","text":"defines input assay specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Assay Specification — assaySpecInput","text":"","code":"assaySpecInput(inputId, label_assays = \"Select Assay\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Assay Specification — assaySpecInput","text":"inputId (string) ID used call module input. label_assays (string) label assay selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Assay Specification — assaySpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Assay Specification — assaySpecServer","title":"Module Server for Assay Specification — assaySpecServer","text":"defines server part assay specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Assay Specification — assaySpecServer","text":"","code":"assaySpecServer(id, assays, exclude_assays = character())"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Assay Specification — assaySpecServer","text":"id (string) shiny module id. assays (reactive character) available assays currently selected experiment. exclude_assays (character) names assays included choices teal module.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Assay Specification — assaySpecServer","text":"chosen assay reactive string.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Assay Specification — assaySpecServer","text":"","code":"ui <- function(id) { ns <- NS(id) teal.widgets::standard_layout( encoding = uiOutput(ns(\"encoding_ui\")), output = textOutput(ns(\"result\")) ) } server <- function(id, data, filter_panel_api) { moduleServer(id, module = function(input, output, session) { output$encoding_ui <- renderUI({ tags$div( experimentSpecInput(session$ns(\"experiment\"), data, \"MAE\"), assaySpecInput( session$ns(\"assay\"), label_assays = \"Please choose assay\" ) ) }) experiment <- experimentSpecServer( id = \"experiment\", data = data, filter_panel_api = filter_panel_api, mae_name = \"MAE\" ) assay <- assaySpecServer( \"assay\", experiment$assays, exclude_assays = c(\"counts\", \"cpm\", \"tpm\", \"bla\") ) output$result <- renderPrint({ assay() }) }) } my_app <- function() { data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init( data = data, modules = modules( module( label = \"assaySpec example\", server = server, ui = ui, datanames = \"all\" ) ) ) shinyApp(app$ui, app$server) } if (interactive()) { my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_adtte_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for ADTTE Variables — assert_adtte_vars","title":"Check for ADTTE Variables — assert_adtte_vars","text":"Check whether x list ADTTE variables.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_adtte_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for ADTTE Variables — assert_adtte_vars","text":"","code":"assert_adtte_vars(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_adtte_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for ADTTE Variables — assert_adtte_vars","text":"x object check.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_adtte_vars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for ADTTE Variables — assert_adtte_vars","text":"","code":"assert_adtte_vars(list(aval = \"AV\", is_event = \"EV\", paramcd = \"PC\", usubjid = \"ID\", avalu = \"u\"))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_summary_funs.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for List of Summary Functions — assert_summary_funs","title":"Check for List of Summary Functions — assert_summary_funs","text":"Check whether x list summary functions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_summary_funs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for List of Summary Functions — assert_summary_funs","text":"","code":"assert_summary_funs(x, null.ok = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_summary_funs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for List of Summary Functions — assert_summary_funs","text":"x object check. null.ok (flag) whether x may also contain NULL, meaning user choice possible summary function applied.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_summary_funs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for List of Summary Functions — assert_summary_funs","text":"","code":"assert_summary_funs(list(mean = colMeans, raw = NULL), null.ok = TRUE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assertion_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Assertion Arguments — assertion_arguments","title":"Standard Assertion Arguments — assertion_arguments","text":"documentation function lists conventional arguments additional checkmate assertions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assertion_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Assertion Arguments — assertion_arguments","text":"x object check. null.ok (flag) whether x may also NULL. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection. info (string) extra information included message testthat reporter, see testthat::expect_that(). label (string) name checked object print messages. Defaults heuristic implemented checkmate::vname().","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assertions.html","id":null,"dir":"Reference","previous_headings":"","what":"Additional Assertions for checkmate — assertions","title":"Additional Assertions for checkmate — assertions","text":"provide additional assertion functions can used together checkmate functions. described individual help pages linked .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assertions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Additional Assertions for checkmate — assertions","text":"Depending function prefix. assert_ functions return object invisibly successful, otherwise throw error message. check_ functions return TRUE successful, otherwise string error message. test_ functions just return TRUE FALSE.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_reactive.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for Reactive Input — check_reactive","title":"Check for Reactive Input — check_reactive","text":"Check whether x reactive input.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_reactive.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for Reactive Input — check_reactive","text":"","code":"check_reactive(x) assert_reactive(x, .var.name = checkmate::vname(x), add = NULL) test_reactive(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_reactive.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for Reactive Input — check_reactive","text":"x object check. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_reactive.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for Reactive Input — check_reactive","text":"","code":"check_reactive(\"bla\") #> [1] FALSE check_reactive(reactive(\"bla\")) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_tag.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for Shiny Tag — check_tag","title":"Check for Shiny Tag — check_tag","text":"Check whether x shiny tag.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_tag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for Shiny Tag — check_tag","text":"","code":"check_tag(x, null.ok = FALSE) assert_tag(x, null.ok = FALSE, .var.name = checkmate::vname(x), add = NULL) test_tag(x, null.ok = FALSE) expect_tag(x, null.ok = FALSE, info = NULL, label = vname(x))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_tag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for Shiny Tag — check_tag","text":"x object check. null.ok (flag) whether x may also NULL. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection. info (string) extra information included message testthat reporter, see testthat::expect_that(). label (string) name checked object print messages. Defaults heuristic implemented checkmate::vname().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_tag.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for Shiny Tag — check_tag","text":"","code":"check_tag(\"bla\") #> [1] \"Must be a 'shiny.tag' or NULL\" check_tag(NULL, null.ok = TRUE) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Experiment Specification — experimentSpecInput","title":"Module Input for Experiment Specification — experimentSpecInput","text":"defines input experiment specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Experiment Specification — experimentSpecInput","text":"","code":"experimentSpecInput( inputId, data, mae_name, label_experiments = \"Select Experiment\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Experiment Specification — experimentSpecInput","text":"inputId (string) ID used call module input. data (reactive)reactive() holding data sets provided app initialization going filters. mae_name (string) name MAE data used teal module. label_experiments (string) label experiment selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Experiment Specification — experimentSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Experiment Specification — experimentSpecServer","title":"Module Server for Experiment Specification — experimentSpecServer","text":"defines server part experiment specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Experiment Specification — experimentSpecServer","text":"","code":"experimentSpecServer( id, data, filter_panel_api, mae_name, name_annotation = \"symbol\", sample_vars_as_factors = TRUE, with_mae_col_data = TRUE )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Experiment Specification — experimentSpecServer","text":"id (string) shiny module id. data (reactive)reactive() holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. mae_name (string) name MAE data used teal module. name_annotation (string NULL) annotation column use name return genes data. NULL, name column set empty strings. sample_vars_as_factors (flag) whether convert sample variables (columns colData() experiment) character factor variables. with_mae_col_data (flag) whether include colData() MAE experiment colData().","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Experiment Specification — experimentSpecServer","text":"List following reactive objects: data: hermes::AnyHermesData experiment. name: name experiment selected user. genes: data.frame genes data, columns id name. assays: names assays data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Experiment Specification — experimentSpecServer","text":"","code":"ui <- function(id, mae_name) { ns <- NS(id) teal.widgets::standard_layout( encoding = uiOutput(ns(\"encoding_ui\")), output = tags$div( verbatimTextOutput(ns(\"summary\")), verbatimTextOutput(ns(\"head\")) ) ) } server <- function(id, data, filter_panel_api, mae_name) { moduleServer(id, function(input, output, session) { output$encoding_ui <- renderUI({ tags$div( experimentSpecInput( session$ns(\"my_experiment\"), data, mae_name, label_experiments = \"Please choose experiment\" ), selectInput( session$ns(\"property\"), \"Please choose property\", c(\"data\", \"name\", \"genes\", \"assays\") ) ) }) experiment <- experimentSpecServer( \"my_experiment\", data, filter_panel_api, mae_name ) result <- reactive({ req(input$property) switch(input$property, data = experiment$data(), name = experiment$name(), genes = experiment$genes(), assays = experiment$assays() ) }) output$summary <- renderPrint({ result <- result() hermes::summary(result) }) output$head <- renderPrint({ result <- result() utils::head(result) }) }) } my_app <- function() { data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init( data = data, modules = modules( module( label = \"experimentSpec example\", server = server, server_args = list(mae_name = \"MAE\"), ui = ui, ui_args = list(mae_name = \"MAE\"), datanames = \"all\" ) ) ) shinyApp(app$ui, app$server) } if (interactive()) { my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/function_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Function Arguments — function_arguments","title":"Standard Function Arguments — function_arguments","text":"documentation function lists conventional arguments functions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/function_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Function Arguments — function_arguments","text":"adtte (data frame) adtte dataset. usubjid_var (string) variable name subject ID variable. mae (MultiAssayExperiment) contains AnyHermesData objects. object (AnyHermesData) contains RNA-seq values one experiment. genes (GeneSpec) specification gene(s) (signature), e.g. using hermes::gene_spec(). experiment_name (string) desired HermesData use. assay_name (string) assay define groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Gene Signature Specification — geneSpecInput","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"defines input gene signature specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"","code":"geneSpecInput( inputId, funs, label_genes = \"Select Gene(s)\", label_funs = \"Select Gene Summary\", label_text_button = \"Enter list of genes\", label_lock_button = \"Lock gene selection (so that it does not get updated when filtering)\", label_select_all_button = paste0(\"Select All Genes (first \", max_options, \")\"), label_select_none_button = \"Select None\", max_options = 200L, max_selected = max_options )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"inputId (string) ID used call module input. funs (named list) names list used function selection drop menu. label_genes (string) label gene selection. label_funs (string) label function selection. label_text_button (string) label text input button. label_lock_button (string) label lock button. label_select_all_button (string) label selecting genes button. label_select_none_button (string) label selecting genes button. max_options (count) maximum number gene options rendering selected via \"Select \". max_selected (count) maximum number genes can selected.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecInput.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"","code":"geneSpecInput(\"my_genes\", list(mean = colMeans), label_funs = \"Please select function\") #>
    #>
    #>
    #>
    + +
    + + - - + + diff --git a/pull_request_template.html b/pull_request_template.html index 45fc6125..21acfbae 100644 --- a/pull_request_template.html +++ b/pull_request_template.html @@ -1,8 +1,22 @@ - -Pull Request • teal.modules.hermes + + + + + + + Skip to contents @@ -18,32 +32,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -60,17 +80,19 @@

    Fixes #nnn

    - + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/reference/adtteSpecInput.html b/reference/adtteSpecInput.html index 015e2663..5c6b0162 100644 --- a/reference/adtteSpecInput.html +++ b/reference/adtteSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for ADTTE Specification — adtteSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
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      +
    + @@ -63,39 +85,47 @@
    -

    Usage

    +

    Usage +

    adtteSpecInput(inputId, label_paramcd = "Select Endpoint")
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    label_paramcd

    (string)
    label for the endpoint (PARAMCD) selection.

    -
    + +
    -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    adtteSpecServer() for the module server and a complete example.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/reference/adtteSpecServer.html b/reference/adtteSpecServer.html index 2149f5c2..478cf21f 100644 --- a/reference/adtteSpecServer.html +++ b/reference/adtteSpecServer.html @@ -1,18 +1,34 @@ - - + + + + + +Module Server for ADTTE Specification — adtteSpecServer • teal.modules.hermes +Module Server for ADTTE Specification — adtteSpecServer • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -28,32 +44,38 @@ + - + + -
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    + @@ -75,7 +97,8 @@
    -

    Usage

    +

    Usage +

    adtteSpecServer(
   id,
   datasets,
@@ -91,8 +114,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    datasets

    (Datasets)
    @@ -105,8 +130,11 @@

    ArgumentsArgumentsArguments -

    Value

    -

    List with the following elements:

    • binned_adtte_subset: reactive containing the joined ADTTE and gene data.

      • +

      Value +

      +

      List with the following elements:

      +
        +

      • binned_adtte_subset: reactive containing the joined ADTTE and gene data.

      • gene_col: reactive containing the string with the column name of the original numeric gene variable.

      • gene_factor: string with the variable name for the binned gene data.

      • time_unit: reactive string with the time unit for the current subset.

        • -

    + +
    -

    See also

    +

    See also +

    adtteSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                datasets) {
   ns <- NS(id)
@@ -235,17 +271,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/assaySpecInput.html b/reference/assaySpecInput.html index 6f94033d..454241fa 100644 --- a/reference/assaySpecInput.html +++ b/reference/assaySpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Assay Specification — assaySpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
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    + @@ -63,39 +85,47 @@
    -

    Usage

    +

    Usage +

    assaySpecInput(inputId, label_assays = "Select Assay")
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    label_assays

    (string)
    label for the assay selection.

    -
    + +
    -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    assaySpecServer() for the module server and a complete example.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/reference/assaySpecServer.html b/reference/assaySpecServer.html index fd286dbb..78dc15ce 100644 --- a/reference/assaySpecServer.html +++ b/reference/assaySpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Assay Specification — assaySpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
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    -

    Usage

    +

    Usage +

    assaySpecServer(id, assays, exclude_assays = character())
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    assays

    (reactive character)
    available assays in the currently selected experiment.

    exclude_assays

    (character)
    names of the assays which should not be included in choices in the teal module.

    -
    + +
    -

    Value

    +

    Value +

    The chosen assay as a reactive string.

    -

    See also

    +

    See also +

    assaySpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                datasets) {
   ns <- NS(id)
@@ -149,17 +178,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/assert_adtte_vars.html b/reference/assert_adtte_vars.html index 4fc39f21..e709e7b7 100644 --- a/reference/assert_adtte_vars.html +++ b/reference/assert_adtte_vars.html @@ -1,10 +1,26 @@ - -Check for ADTTE Variables — assert_adtte_vars • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
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    -

    Usage

    +

    Usage +

    assert_adtte_vars(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    -
    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    assert_adtte_vars(list(aval = "AV", is_event = "EV", paramcd = "PC", usubjid = "ID", avalu = "u"))
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/reference/assert_summary_funs.html b/reference/assert_summary_funs.html index e53b03ff..c8d2371c 100644 --- a/reference/assert_summary_funs.html +++ b/reference/assert_summary_funs.html @@ -1,10 +1,26 @@ - -Check for List of Summary Functions — assert_summary_funs • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
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    -

    Usage

    +

    Usage +

    assert_summary_funs(x, null.ok = FALSE)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    null.ok

    (flag)
    whether x may also contain NULL, meaning that a user choice is possible where no summary function should be applied.

    -
    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    assert_summary_funs(list(mean = colMeans, raw = NULL), null.ok = TRUE)
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/reference/assertion_arguments.html b/reference/assertion_arguments.html index 3c2a3120..b2f2a42c 100644 --- a/reference/assertion_arguments.html +++ b/reference/assertion_arguments.html @@ -1,10 +1,26 @@ - -Standard Assertion Arguments — assertion_arguments • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
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        +
        • -
      +
    + @@ -64,8 +86,10 @@
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    null.ok

    (flag)
    whether x may also be NULL.

    @@ -81,19 +105,22 @@

    Argumentscheckmate::vname().

    -

    + + - + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/reference/assertions.html b/reference/assertions.html index 1befeefc..2ed492d8 100644 --- a/reference/assertions.html +++ b/reference/assertions.html @@ -1,14 +1,30 @@ - - + + + + + +Additional Assertions for checkmate — assertions • teal.modules.hermes +Additional Assertions for checkmate — assertions • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,39 +40,46 @@ + - + + -
    • +
        +
        • -
      +
    +
    -

    Additional Assertions for checkmate

    +

    Additional Assertions for checkmate +

    Source: R/checkmate.R
    assertions.Rd
    @@ -70,30 +93,37 @@
    -

    Value

    -

    Depending on the function prefix.

    • assert_ functions return the object invisibly if successful, and otherwise +

      Value +

      +

      Depending on the function prefix.

      +
        +

      • assert_ functions return the object invisibly if successful, and otherwise throw an error message.

      • check_ functions return TRUE if successful, otherwise a string with the error message.

      • test_ functions just return TRUE or FALSE.

        • -
    + +
    -

    See also

    +

    See also +

    assert_tag(), assert_reactive(), assert_summary_funs(), assert_adtte_vars()

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/reference/check_reactive.html b/reference/check_reactive.html index 15b5f575..93ef3e85 100644 --- a/reference/check_reactive.html +++ b/reference/check_reactive.html @@ -1,10 +1,26 @@ - -Check for Reactive Input — check_reactive • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    check_reactive(x)
 
 assert_reactive(x, .var.name = checkmate::vname(x), add = NULL)
@@ -72,8 +95,10 @@ 
    Usage
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    .var.name

    (string)
    name of the checked object to print in @@ -81,14 +106,17 @@

    Argumentscheckmate::AssertCollection.

    -
    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    check_reactive("bla")
 #> [1] FALSE
 check_reactive(reactive("bla"))
@@ -96,17 +124,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/check_tag.html b/reference/check_tag.html index 197abc32..f2f18d15 100644 --- a/reference/check_tag.html +++ b/reference/check_tag.html @@ -1,10 +1,26 @@ - -Check for Shiny Tag — check_tag • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    check_tag(x, null.ok = FALSE)
 
 assert_tag(x, null.ok = FALSE, .var.name = checkmate::vname(x), add = NULL)
@@ -74,8 +97,10 @@ 
    Usage
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    null.ok

    (flag)
    whether x may also be NULL.

    @@ -91,14 +116,17 @@

    Argumentscheckmate::vname().

    -

    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    check_tag("bla")
 #> [1] "Must be a 'shiny.tag' or NULL"
 check_tag(NULL, null.ok = TRUE)
@@ -106,17 +134,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/experimentSpecInput.html b/reference/experimentSpecInput.html index f344681b..f90be477 100644 --- a/reference/experimentSpecInput.html +++ b/reference/experimentSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Experiment Specification — experimentSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    experimentSpecInput(
   inputId,
   datasets,
@@ -73,8 +96,10 @@ 
    Usage
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    datasets
    @@ -86,28 +111,33 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    experimentSpecServer() for the module server and a complete example.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/reference/experimentSpecServer.html b/reference/experimentSpecServer.html index c4bc0c88..d1062546 100644 --- a/reference/experimentSpecServer.html +++ b/reference/experimentSpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Experiment Specification — experimentSpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    experimentSpecServer(
   id,
   datasets,
@@ -75,8 +98,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    datasets

    (Datasets)
    @@ -95,21 +120,28 @@

    Arguments -

    Value

    -

    List with the following reactive objects:

    • data: the hermes::AnyHermesData experiment.

      • +

      Value +

      +

      List with the following reactive objects:

      +
        +

      • data: the hermes::AnyHermesData experiment.

      • name: the name of the experiment as selected by the user.

      • genes: a data.frame with the genes in data, with columns id and name.

      • assays: the names of the assays in data.

        • -

    + +
    -

    See also

    +

    See also +

    experimentSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                datasets,
                mae_name) {
@@ -189,17 +221,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/function_arguments.html b/reference/function_arguments.html index d3f09c44..d44fb139 100644 --- a/reference/function_arguments.html +++ b/reference/function_arguments.html @@ -1,10 +1,26 @@ - -Standard Function Arguments — function_arguments • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -64,8 +86,10 @@
    -

    Arguments

    -
    adtte
    +

    Arguments +

    +
    +
    adtte

    (data frame)
    an adtte dataset.

    usubjid_var

    (string)
    variable name of the subject ID variable.

    @@ -80,19 +104,22 @@

    Arguments

    teal.modules.hermes is a part of the NEST and pharmaverse.

    - + + - - + + diff --git a/reference/geneSpecInput.html b/reference/geneSpecInput.html index 94989a00..dcb65873 100644 --- a/reference/geneSpecInput.html +++ b/reference/geneSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Gene Signature Specification — geneSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    geneSpecInput(
   inputId,
   funs,
@@ -80,8 +103,10 @@ 
    Usage
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    funs
    @@ -104,18 +129,22 @@

    Arguments
    max_selected

    (count)
    maximum number of genes which can be selected.

    -

    + +
    -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    geneSpecServer() for the module server and a complete example.

    -

    Examples

    +

    Examples +

    geneSpecInput("my_genes", list(mean = colMeans), label_funs = "Please select function")
 #> <div class="row">
 #>   <div class="col-sm-8">
@@ -277,17 +306,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/geneSpecServer.html b/reference/geneSpecServer.html index f74883d7..6c5d1aac 100644 --- a/reference/geneSpecServer.html +++ b/reference/geneSpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Gene Signature Specification — geneSpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    geneSpecServer(
   id,
   funs,
@@ -76,8 +99,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    funs

    (static named list)
    names of this list will be used for the function @@ -89,19 +114,23 @@

    Arguments -

    Value

    +

    Value +

    Reactive hermes::GeneSpec which can be used as input for the relevant hermes functions.

    -

    See also

    +

    See also +

    geneSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                datasets,
                funs) {
@@ -173,17 +202,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/h_assign_to_group_list.html b/reference/h_assign_to_group_list.html index b17ef6c3..f02616ee 100644 --- a/reference/h_assign_to_group_list.html +++ b/reference/h_assign_to_group_list.html @@ -1,12 +1,28 @@ - - + + + + + +Helper Function For Group List Creation — h_assign_to_group_list • teal.modules.hermes +Helper Function For Group List Creation — h_assign_to_group_list • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,22 +88,28 @@
    -

    Usage

    +

    Usage +

    h_assign_to_group_list(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (named list of character)
    input assignment list.

    -
    + +
    -

    Value

    +

    Value +

    A combination list.

    -

    Examples

    +

    Examples +

    assign_list <- list(
   "ASIAN" = "1",
   "BLACK OR AFRICAN AMERICAN" = "1",
@@ -99,17 +127,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/h_collapse_levels.html b/reference/h_collapse_levels.html index ddd01705..d2a578e3 100644 --- a/reference/h_collapse_levels.html +++ b/reference/h_collapse_levels.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function for Collapsing of Factor Levels — h_collapse_levels • teal.modules.hermes +Helper Function for Collapsing of Factor Levels — h_collapse_levels • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,32 +40,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,25 +91,31 @@
    -

    Usage

    +

    Usage +

    h_collapse_levels(x, group_list)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (factor)
    original factor.

    group_list

    (named list of character)
    includes the collapsing specification.

    -
    + +
    -

    Value

    +

    Value +

    The transformed factor x with new levels.

    -

    Examples

    +

    Examples +

    set.seed(123)
 x <- factor(sample(
   c("ASIAN", "BLACK OR AFRICAN AMERICAN", "MULTIPLE", "UNKNOWN", "WHITE"),
@@ -104,17 +132,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/h_extract_words.html b/reference/h_extract_words.html index 10d7d349..a5cbca74 100644 --- a/reference/h_extract_words.html +++ b/reference/h_extract_words.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Extract Words — h_extract_words • teal.modules.hermes +Helper Function to Extract Words — h_extract_words • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,32 +40,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,22 +91,28 @@
    -

    Usage

    +

    Usage +

    h_extract_words(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (string)
    input.

    -
    + +
    -

    Value

    +

    Value +

    Character vector with the extracted words.

    -

    Examples

    +

    Examples +

    h_extract_words("a, b, , c, 234; 34562 - GeneID:bla")
 #> [1] "a"          "b"          "c"          "234"        "34562"     
 #> [6] "GeneID:bla"
@@ -93,17 +121,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/h_gene_data.html b/reference/h_gene_data.html index 7e7961ff..9835e27e 100644 --- a/reference/h_gene_data.html +++ b/reference/h_gene_data.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Format Gene Choices — h_gene_data • teal.modules.hermes +Helper Function to Format Gene Choices — h_gene_data • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,32 +40,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,33 +91,40 @@
    -

    Usage

    +

    Usage +

    h_gene_data(object, name_annotation)
    -

    Arguments

    -
    object
    +

    Arguments +

    +
    +
    object

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    name_annotation

    (string or NULL)
    which annotation column to use as name to return in the genes data. If NULL, then the name column will be set to empty strings.

    -
    + +
    -

    Value

    +

    Value +

    A data.frame with id and name columns containing all genes from object.

    -

    Details

    +

    Details +

    Note that missing names or names that only contain whitespace are replaced by empty strings for consistency and better labeling in the UI downstream

    -

    Examples

    +

    Examples +

    object <- hermes::hermes_data[1:10, ]
 h_gene_data(object, "symbol")
 #>                  id         name
@@ -112,17 +141,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/h_km_mae_to_adtte.html b/reference/h_km_mae_to_adtte.html index dc4ffcc6..15db60e8 100644 --- a/reference/h_km_mae_to_adtte.html +++ b/reference/h_km_mae_to_adtte.html @@ -1,10 +1,26 @@ - -Data Preprocessing for ADTTE Module — h_km_mae_to_adtte • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    h_km_mae_to_adtte(
   adtte,
   mae,
@@ -75,8 +98,10 @@ 
    Usage
    -

    Arguments

    -
    adtte
    +

    Arguments +

    +
    +
    adtte

    (data frame)
    an adtte dataset.

    mae

    (MultiAssayExperiment)
    contains AnyHermesData objects.

    @@ -89,22 +114,26 @@

    Arguments -

    Value

    +

    Value +

    A data frame containing all columns/rows from adtte that match by subject ID with the row names of the MAE and have the gene samples available in the given experiment. The attribute gene_cols contains the column names for the gene columns.

    -

    Note

    +

    Note +

    The final gene column names can start with a different string than the original gene IDs (or labels), in particular white space and colons are removed.

    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 adtte <- scda::synthetic_cdisc_data("rcd_2021_07_07")$adtte %>%
   dplyr::mutate(CNSR = as.logical(CNSR))
@@ -130,17 +159,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/h_order_genes.html b/reference/h_order_genes.html index a5b51c84..df8c465b 100644 --- a/reference/h_order_genes.html +++ b/reference/h_order_genes.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Order Gene Choices — h_order_genes • teal.modules.hermes +Helper Function to Order Gene Choices — h_order_genes • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,32 +40,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,23 +91,29 @@
    -

    Usage

    +

    Usage +

    h_order_genes(genes)
    -

    Arguments

    -
    genes
    +

    Arguments +

    +
    +
    genes

    (data.frame)
    containing id and name columns of the gene choices. Note that no missing values are allowed.

    -
    + +
    -

    Value

    +

    Value +

    The ordered data.frame.

    -

    Examples

    +

    Examples +

    genes <- data.frame(
   id = c("7", "1", "2", "345346", "0"),
   name = c("e", "", "c", "", "a")
@@ -100,17 +128,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/h_parse_genes.html b/reference/h_parse_genes.html index 83233df2..e74f987c 100644 --- a/reference/h_parse_genes.html +++ b/reference/h_parse_genes.html @@ -1,12 +1,28 @@ - - + + + + + +Helper Function to Parse Genes — h_parse_genes • teal.modules.hermes +Helper Function to Parse Genes — h_parse_genes • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,25 +88,31 @@
    -

    Usage

    +

    Usage +

    h_parse_genes(words, choices)
    -

    Arguments

    -
    words
    +

    Arguments +

    +
    +
    words

    (character)
    containing gene IDs or names.

    choices

    (data.frame)
    containing id and name columns of the new choices.

    -
    + +
    -

    Value

    +

    Value +

    The subset of choices which matches words in ID or name.

    -

    Examples

    +

    Examples +

    h_parse_genes(
   c("a", "2535"),
   data.frame(id = as.character(2533:2537), name = letters[1:5])
@@ -95,17 +123,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/h_update_gene_selection.html b/reference/h_update_gene_selection.html index eee4dc4e..f2b262ad 100644 --- a/reference/h_update_gene_selection.html +++ b/reference/h_update_gene_selection.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Update Gene Selection — h_update_gene_selection • teal.modules.hermes +Helper Function to Update Gene Selection — h_update_gene_selection • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,32 +40,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,13 +91,16 @@
    -

    Usage

    +

    Usage +

    h_update_gene_selection(session, inputId, selected, choices)
    -

    Arguments

    -
    session
    +

    Arguments +

    +
    +
    session

    (ShinySession)
    the session object.

    inputId

    (string)
    @@ -85,20 +110,23 @@

    Arguments

    + + + + - - + + diff --git a/reference/heatmap_plot.html b/reference/heatmap_plot.html index 3da35ac4..b01fbb83 100644 --- a/reference/heatmap_plot.html +++ b/reference/heatmap_plot.html @@ -1,10 +1,26 @@ - -Correlation Heatmap Plot — heatmap_plot • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,24 +85,30 @@
    -

    Usage

    +

    Usage +

    heatmap_plot(object, assay_name)
    -

    Arguments

    -
    object
    +

    Arguments +

    +
    +
    object

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    assay_name

    (string)
    the assay to define the groups.

    -
    + +
    -

    Value

    +

    Value +

    Plot to be displayed in the teal app.

    -

    Examples

    +

    Examples +

    library(hermes)
 #> Loading required package: ggfortify
 #> Loading required package: SummarizedExperiment
@@ -153,17 +181,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/include_css_files.html b/reference/include_css_files.html index 65263987..bfce8d07 100644 --- a/reference/include_css_files.html +++ b/reference/include_css_files.html @@ -1,12 +1,28 @@ - - + + + + + +Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.modules.hermes +Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,32 +88,39 @@
    -

    Usage

    +

    Usage +

    include_css_files(pattern = "*")
    -

    Arguments

    -
    pattern
    +

    Arguments +

    +
    +
    pattern

    (character) pattern of files to be included

    -
    + +
    -

    Value

    +

    Value +

    HTML code that includes CSS files

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/reference/include_js_files.html b/reference/include_js_files.html index b05ac26c..003ade2e 100644 --- a/reference/include_js_files.html +++ b/reference/include_js_files.html @@ -1,12 +1,28 @@ - - + + + + + +Include JS files from /inst/js/ package directory to application header — include_js_files • teal.modules.hermes +Include JS files from /inst/js/ package directory to application header — include_js_files • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,34 +88,41 @@
    -

    Usage

    +

    Usage +

    include_js_files(pattern = "*")
    -

    Arguments

    -
    pattern
    +

    Arguments +

    +
    +
    pattern

    (character) pattern of files to be included, passed to system.file

    except

    (character) vector of basename filenames to be excluded

    -
    + +
    -

    Value

    +

    Value +

    HTML code that includes JS files

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/reference/index.html b/reference/index.html index af9372cd..dc65826c 100644 --- a/reference/index.html +++ b/reference/index.html @@ -1,8 +1,22 @@ - -Function reference • teal.modules.hermes + + + + + + + Skip to contents @@ -18,32 +32,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -54,280 +74,377 @@
    -

    Package

    +

    Package +

    -
    +
    +
    -
    +
    +
    teal.modules.hermes-package
    -
    teal.modules.hermes Package
    -
    -

    Utility Functions

    +
    +teal.modules.hermes Package
    + +
    +
    +

    Utility Functions +

    -
    +
    +
    -
    +
    +
    h_assign_to_group_list()
    Helper Function For Group List Creation
    -
    +
    +
    +
    h_collapse_levels()
    Helper Function for Collapsing of Factor Levels
    -
    +
    +
    +
    h_extract_words()
    Helper Function to Extract Words
    -
    +
    +
    +
    h_gene_data()
    Helper Function to Format Gene Choices
    -
    +
    +
    +
    h_km_mae_to_adtte()
    Data Preprocessing for ADTTE Module
    -
    +
    +
    +
    h_order_genes()
    Helper Function to Order Gene Choices
    -
    +
    +
    +
    h_parse_genes()
    Helper Function to Parse Genes
    -
    +
    +
    +
    h_update_gene_selection()
    Helper Function to Update Gene Selection
    -
    +
    +
    +
    is_blank()
    Checking for Empty String
    -
    -

    Shiny Modules

    + +
    +
    +

    Shiny Modules +

    -
    +
    +
    -
    +
    +
    adtteSpecInput()
    Module Input for ADTTE Specification
    -
    +
    +
    +
    adtteSpecServer()
    Module Server for ADTTE Specification
    -
    +
    +
    +
    assaySpecInput()
    Module Input for Assay Specification
    -
    +
    +
    +
    assaySpecServer()
    Module Server for Assay Specification
    -
    +
    +
    +
    experimentSpecInput()
    Module Input for Experiment Specification
    -
    +
    +
    +
    experimentSpecServer()
    Module Server for Experiment Specification
    -
    +
    +
    +
    geneSpecInput()
    Module Input for Gene Signature Specification
    -
    +
    +
    +
    geneSpecServer()
    Module Server for Gene Signature Specification
    -
    +
    +
    +
    sampleVarSpecInput()
    Module Input for Sample Variable Specification
    -
    +
    +
    +
    sampleVarSpecServer()
    Module Server for Sample Variable Specification
    -
    +
    +
    +
    multiSampleVarSpecServer()
    Module Server for Specification of Multiple Sample Variables
    -
    -

    Teal Module Functions

    + +
    +
    +

    Teal Module Functions +

    -
    +
    +
    -
    +
    +
    tm_g_barplot() ui_g_barplot() srv_g_barplot() sample_tm_g_barplot()
    Teal Module for RNA-seq Barplot
    -
    +
    +
    +
    tm_g_boxplot() ui_g_boxplot() srv_g_boxplot() sample_tm_g_boxplot()
    Teal Module for RNA-seq Boxplot
    -
    +
    +
    +
    tm_g_forest_tte() ui_g_forest_tte() srv_g_forest_tte() sample_tm_g_forest_tte()
    Teal Module for Survival Forest Plot
    -
    +
    +
    +
    tm_g_km() ui_g_km() srv_g_km() sample_tm_g_km()
    Teal Module for Kaplan-Meier Plot
    -
    +
    +
    +
    tm_g_pca() ui_g_pca() srv_g_pca() sample_tm_g_pca()
    Teal Module for PCA Analysis
    -
    +
    +
    +
    tm_g_quality() ui_g_quality() srv_g_quality() sample_tm_g_quality()
    Teal Module for RNA-seq Quality Control
    -
    +
    +
    +
    tm_g_scatterplot() ui_g_scatterplot() srv_g_scatterplot() sample_tm_g_scatterplot()
    Teal Module for RNA-seq Scatterplot
    -
    +
    +
    +
    tm_g_volcanoplot() ui_g_volcanoplot() srv_g_volcanoplot() sample_tm_g_volcanoplot()
    Teal Module for RNA-seq Volcano Plot
    -
    -

    Graph Functions

    + +
    +
    +

    Graph Functions +

    -
    +
    +
    -
    +
    +
    heatmap_plot()
    Correlation Heatmap Plot
    -
    +
    +
    +
    top_gene_plot()
    Most Expressed Genes Plot
    -
    -

    Assertions

    + +
    +
    +

    Assertions +

    -
    +
    +
    -
    +
    +
    assert_adtte_vars()
    Check for ADTTE Variables
    -
    +
    +
    +
    check_reactive() assert_reactive() test_reactive()
    Check for Reactive Input
    -
    +
    +
    +
    assert_summary_funs()
    Check for List of Summary Functions
    -
    +
    +
    +
    check_tag() assert_tag() test_tag() expect_tag()
    Check for Shiny Tag
    -
    -

    Validations

    + +
    +
    +

    Validations +

    -
    +
    +
    -
    +
    +
    validate_gene_spec()
    Validation of Gene Specification
    -
    +
    +
    +
    validate_n_levels()
    Validation of Number of Levels
    -
    + + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/reference/is_blank.html b/reference/is_blank.html index 0f27d47a..e6fb8f1a 100644 --- a/reference/is_blank.html +++ b/reference/is_blank.html @@ -1,12 +1,28 @@ - - + + + + + +Checking for Empty String — is_blank • teal.modules.hermes +Checking for Empty String — is_blank • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,22 +88,28 @@
    -

    Usage

    +

    Usage +

    is_blank(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    object to check.

    -
    + +
    -

    Value

    +

    Value +

    Flag whether x is identical to an empty string, i.e. "".

    -

    Examples

    +

    Examples +

    is_blank("")
 #> [1] TRUE
 is_blank(" ")
@@ -89,17 +117,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/module_arguments.html b/reference/module_arguments.html index 4761871e..fb01f21c 100644 --- a/reference/module_arguments.html +++ b/reference/module_arguments.html @@ -1,10 +1,26 @@ - -Standard Module Arguments — module_arguments • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -64,8 +86,10 @@
    -

    Arguments

    -
    datasets
    +

    Arguments +

    +
    +
    datasets

    (Datasets)
    teal specific argument which is automatically passed to the UI and server functions, holding all the data sets provided in the app initialization.

    @@ -79,8 +103,11 @@

    ArgumentsArgumentsArguments

    teal.modules.hermes is a part of the NEST and pharmaverse.

    - + + - - + + diff --git a/reference/multiSampleVarSpecServer.html b/reference/multiSampleVarSpecServer.html index dffdd5c8..32adcfe9 100644 --- a/reference/multiSampleVarSpecServer.html +++ b/reference/multiSampleVarSpecServer.html @@ -1,12 +1,28 @@ - - + + + + + +Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer • teal.modules.hermes +Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,13 +88,16 @@
    -

    Usage

    +

    Usage +

    multiSampleVarSpecServer(inputIds, original_data, ...)
    -

    Arguments

    -
    inputIds
    +

    Arguments +

    +
    +
    inputIds

    (character)
    multiple input IDs corresponding to the different sample variables specified in the UI function.

    original_data
    @@ -85,30 +110,35 @@

    Arguments -

    Value

    +

    Value +

    List with the final transformed experiment_data reactive and a list vars which contains the selected sample variables as reactives under their input ID.

    -

    Examples

    +

    Examples +

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/reference/sampleVarSpecInput.html b/reference/sampleVarSpecInput.html index d1389fdf..2d1ef657 100644 --- a/reference/sampleVarSpecInput.html +++ b/reference/sampleVarSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Sample Variable Specification — sampleVarSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    sampleVarSpecInput(
   inputId,
   label_vars = "Select sample variable",
@@ -72,26 +95,32 @@ 
    Usage
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    label_vars

    (string)
    label for the sample variable selection.

    label_levels_button

    (string)
    label for the levels combination button.

    -
    + +
    -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    sampleVarSpecServer() for the module server and a complete example.

    -

    Examples

    +

    Examples +

    sampleVarSpecInput("my_vars", label_vars = "Select faceting variable")
 #> <div class="row">
 #>   <div class="col-sm-8">
@@ -210,17 +239,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/sampleVarSpecServer.html b/reference/sampleVarSpecServer.html index aecd594c..3a3e5603 100644 --- a/reference/sampleVarSpecServer.html +++ b/reference/sampleVarSpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Sample Variable Specification — sampleVarSpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    sampleVarSpecServer(
   id,
   experiment_name,
@@ -77,8 +100,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    experiment_name

    (reactive string)
    name of the input experiment.

    @@ -100,25 +125,30 @@

    Arguments -

    Value

    +

    Value +

    Reactive SummarizedExperiment::SummarizedExperiment which can be used as input for the relevant hermes functions.

    -

    Note

    +

    Note +

    Only atomic columns (e.g. not DataFrame columns) of the colData which are not completely missing (NA) will be shown for selection. If num_levels is specified then only factor columns will be available.

    -

    See also

    +

    See also +

    sampleVarSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                datasets) {
   ns <- NS(id)
@@ -184,17 +214,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/teal.modules.hermes-package.html b/reference/teal.modules.hermes-package.html index a44f768c..5e509b8e 100644 --- a/reference/teal.modules.hermes-package.html +++ b/reference/teal.modules.hermes-package.html @@ -1,10 +1,26 @@ - -teal.modules.hermes Package — teal.modules.hermes-package • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,39 +36,46 @@ + - + + -
    • +
        +
        • -
      +
    +
    -

    teal.modules.hermes Package

    +

    +teal.modules.hermes Package

    Source: R/package.R
    teal.modules.hermes-package.Rd
    @@ -64,15 +87,23 @@
    -

    See also

    -

    Useful links:

    +
    -

    Author

    +

    Author +

    Maintainer: Daniel Sabanés Bové daniel.sabanes_bove@roche.com

    -

    Authors:

    • Nikolas Burkoff

      • +

      Authors:

      +
        +

      • Nikolas Burkoff

      • Dinakar Kulkarni

      • Konrad Pagacz

      • Namrata Bhatia

        • @@ -82,25 +113,31 @@

        Author<

      • Stefanie Bienert

      • Haocheng Li

      • Lyndsee Midori Zhang

        • -

      Other contributors:

      • Sorin Voicu [contributor]

        • +
      +

      Other contributors:

      +
        +

      • Sorin Voicu [contributor]

      • Benoit Falquet [contributor]

      • Mahmoud Hallal [contributor]

      • Tim Treis [contributor]

      • F. Hoffmann-La Roche AG [copyright holder, funder]

        • -
    + +
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/reference/tm_g_barplot.html b/reference/tm_g_barplot.html index 2555da97..680858d2 100644 --- a/reference/tm_g_barplot.html +++ b/reference/tm_g_barplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Barplot — tm_g_barplot • teal.modules.hermes +Teal Module for RNA-seq Barplot — tm_g_barplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    tm_g_barplot(
   label,
   mae_name,
@@ -85,8 +108,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    mae_name
    @@ -112,21 +137,27 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_barplot: sets up the user interface.

      • +
        +

      • ui_g_barplot: sets up the user interface.

      • srv_g_barplot: sets up the server with reactive graph.

      • sample_tm_g_barplot: sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -151,17 +182,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/tm_g_boxplot.html b/reference/tm_g_boxplot.html index 5d580c34..031c86b9 100644 --- a/reference/tm_g_boxplot.html +++ b/reference/tm_g_boxplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Boxplot — tm_g_boxplot • teal.modules.hermes +Teal Module for RNA-seq Boxplot — tm_g_boxplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    tm_g_boxplot(
   label,
   mae_name,
@@ -85,8 +108,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    mae_name
    @@ -112,21 +137,27 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_boxplot: sets up the user interface.

      • +
        +

      • ui_g_boxplot: sets up the user interface.

      • srv_g_boxplot: sets up the server with reactive graph.

      • sample_tm_g_boxplot: sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -151,17 +182,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/tm_g_forest_tte.html b/reference/tm_g_forest_tte.html index 6db5364a..85c6a05d 100644 --- a/reference/tm_g_forest_tte.html +++ b/reference/tm_g_forest_tte.html @@ -1,10 +1,26 @@ - -Teal Module for Survival Forest Plot — tm_g_forest_tte • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    tm_g_forest_tte(
   label,
   adtte_name,
@@ -105,8 +128,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    adtte_name
    @@ -116,8 +141,11 @@

    ArgumentsArgumentsArguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_forest_tte: sets up the user interface.

      • +
        +

      • ui_g_forest_tte: sets up the user interface.

      • srv_g_forest_tte: sets up the server with reactive graph.

      • sample_tm_g_forest_tte: sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 adtte <- scda::synthetic_cdisc_data("rcd_2021_07_07")$adtte %>%
   dplyr::mutate(is_event = (.data$CNSR == 0))
@@ -202,17 +237,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/tm_g_km.html b/reference/tm_g_km.html index 6d46be41..a8214cce 100644 --- a/reference/tm_g_km.html +++ b/reference/tm_g_km.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for Kaplan-Meier Plot — tm_g_km • teal.modules.hermes +Teal Module for Kaplan-Meier Plot — tm_g_km • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    tm_g_km(
   label,
   adtte_name,
@@ -104,8 +127,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    adtte_name
    @@ -115,8 +140,11 @@

    ArgumentsArgumentsArguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_km: sets up the user interface.

      • +
        +

      • ui_g_km: sets up the user interface.

      • srv_g_km: sets up the user interface.

      • sample_tm_g_km: sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 adtte <- scda::synthetic_cdisc_data("rcd_2021_07_07")$adtte %>%
   dplyr::mutate(is_event = (.data$CNSR == 0))
@@ -199,17 +234,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/tm_g_pca.html b/reference/tm_g_pca.html index 51a22660..55b06126 100644 --- a/reference/tm_g_pca.html +++ b/reference/tm_g_pca.html @@ -1,14 +1,30 @@ - - + + + + + +Teal Module for PCA Analysis — tm_g_pca • teal.modules.hermes +Teal Module for PCA Analysis — tm_g_pca • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,32 +40,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_pca(
   label,
   mae_name,
@@ -86,8 +109,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    mae_name
    @@ -109,21 +134,27 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_pca: sets up the user interface.

      • +
        +

      • ui_g_pca: sets up the user interface.

      • srv_g_pca: sets up the server with reactive graph.

      • sample_tm_g_pca: sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -148,17 +179,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/tm_g_quality.html b/reference/tm_g_quality.html index e2e20409..e9dc59dc 100644 --- a/reference/tm_g_quality.html +++ b/reference/tm_g_quality.html @@ -1,14 +1,30 @@ - - + + + + + +Teal Module for RNA-seq Quality Control — tm_g_quality • teal.modules.hermes +Teal Module for RNA-seq Quality Control — tm_g_quality • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,32 +40,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_quality(
   label,
   mae_name,
@@ -86,8 +109,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    mae_name
    @@ -109,21 +134,27 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_quality: sets up the user interface.

      • +
        +

      • ui_g_quality: sets up the user interface.

      • srv_g_quality: sets up the server with reactive graphs.

      • sample_tm_g_quality: sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -147,17 +178,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/tm_g_scatterplot.html b/reference/tm_g_scatterplot.html index 6fc6f28d..cb761922 100644 --- a/reference/tm_g_scatterplot.html +++ b/reference/tm_g_scatterplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Scatterplot — tm_g_scatterplot • teal.modules.hermes +Teal Module for RNA-seq Scatterplot — tm_g_scatterplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    tm_g_scatterplot(
   label,
   mae_name,
@@ -85,8 +108,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    mae_name
    @@ -112,21 +137,27 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_scatterplot: sets up the user interface.

      • +
        +

      • ui_g_scatterplot: sets up the user interface.

      • srv_g_scatterplot: sets up the server with reactive graph.

      • sample_tm_g_scatterplot: sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -151,17 +182,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/tm_g_volcanoplot.html b/reference/tm_g_volcanoplot.html index 7feef240..5c89e97b 100644 --- a/reference/tm_g_volcanoplot.html +++ b/reference/tm_g_volcanoplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot • teal.modules.hermes +Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    tm_g_volcanoplot(
   label,
   mae_name,
@@ -83,8 +106,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    mae_name
    @@ -106,21 +131,27 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_volcanoplot: sets up the user interface.

      • +
        +

      • ui_g_volcanoplot: sets up the user interface.

      • srv_g_volcanoplot: sets up the server with reactive graph.

      • sample_tm_g_volcanoplot: sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -145,17 +176,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/reference/top_gene_plot.html b/reference/top_gene_plot.html index 76f471aa..04c5289d 100644 --- a/reference/top_gene_plot.html +++ b/reference/top_gene_plot.html @@ -1,10 +1,26 @@ - -Most Expressed Genes Plot — top_gene_plot • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,41 +85,49 @@
    -

    Usage

    +

    Usage +

    top_gene_plot(object, assay_name)
    -

    Arguments

    -
    object
    +

    Arguments +

    +
    +
    object

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    assay_name

    (string)
    the assay to define the groups.

    -
    + +
    -

    Value

    +

    Value +

    Plot to be displayed in the teal app.

    -

    Examples

    +

    Examples +

    library(hermes)
 object <- HermesData(summarized_experiment)
 result <- top_gene_plot(object, assay_name = "counts")
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/reference/validate_gene_spec.html b/reference/validate_gene_spec.html index 61ea1e40..06a1bf4e 100644 --- a/reference/validate_gene_spec.html +++ b/reference/validate_gene_spec.html @@ -1,12 +1,28 @@ - - + + + + + +Validation of Gene Specification — validate_gene_spec • teal.modules.hermes +Validation of Gene Specification — validate_gene_spec • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,30 +88,36 @@
    -

    Usage

    +

    Usage +

    validate_gene_spec(gene_spec, gene_choices)
    -

    Arguments

    -
    gene_spec
    +

    Arguments +

    +
    +
    gene_spec

    (GeneSpec)
    gene specification.

    gene_choices

    (character)
    all possible gene choices.

    -
    + + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/reference/validate_n_levels.html b/reference/validate_n_levels.html index 611a0a6d..ef0d8136 100644 --- a/reference/validate_n_levels.html +++ b/reference/validate_n_levels.html @@ -1,12 +1,28 @@ - - + + + + + +Validation of Number of Levels — validate_n_levels • teal.modules.hermes +Validation of Number of Levels — validate_n_levels • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,32 +88,38 @@
    -

    Usage

    +

    Usage +

    validate_n_levels(x, name, n_levels)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (factor)
    factor to validate.

    name

    (string)
    name of x in the app.

    n_levels

    (count)
    required number of factor levels in x.

    -
    + + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/404.html b/v0.1.4/404.html index 9d0f2497..aabd8ea5 100644 --- a/v0.1.4/404.html +++ b/v0.1.4/404.html @@ -1,5 +1,4 @@ - - + @@ -41,14 +40,15 @@ Changelog
  • -
    main + +
    + main latest-tag v0.1.6 v0.1.5 -v0.1.4
    • +v0.1.4 + + + + -
    • +
        +
        • -
      +
    + @@ -57,65 +77,80 @@
    -

    Our Pledge

    +

    Our Pledge +

    We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.

    We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.

    -

    Our Standards

    +

    Our Standards +

    Examples of behavior that contributes to a positive environment for our community include:

    -
    • Demonstrating empathy and kindness toward other people
      • +
        +
      • Demonstrating empathy and kindness toward other people
      • Being respectful of differing opinions, viewpoints, and experiences
      • Giving and gracefully accepting constructive feedback
      • Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
      • Focusing on what is best not just for us as individuals, but for the overall community
        • -

      Examples of unacceptable behavior include:

      -
      • The use of sexualized language or imagery, and sexual attention or advances of any kind
        • +
      +

      Examples of unacceptable behavior include:

      +
        +
      • The use of sexualized language or imagery, and sexual attention or advances of any kind
      • Trolling, insulting or derogatory comments, and personal or political attacks
      • Public or private harassment
      • Publishing others’ private information, such as a physical or email address, without their explicit permission
      • Other conduct which could reasonably be considered inappropriate in a professional setting
        • -
    + +
    -

    Enforcement Responsibilities

    +

    Enforcement Responsibilities +

    Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.

    Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.

    -

    Scope

    +

    Scope +

    This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.

    -

    Enforcement

    +

    Enforcement +

    Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at [INSERT CONTACT METHOD]. All complaints will be reviewed and investigated promptly and fairly.

    All community leaders are obligated to respect the privacy and security of the reporter of any incident.

    -

    Enforcement Guidelines

    +

    Enforcement Guidelines +

    Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:

    -

    1. Correction

    +

    1. Correction +

    Community Impact: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.

    Consequence: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.

    -

    2. Warning

    +

    2. Warning +

    Community Impact: A violation through a single incident or series of actions.

    Consequence: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.

    -

    3. Temporary Ban

    +

    3. Temporary Ban +

    Community Impact: A serious violation of community standards, including sustained inappropriate behavior.

    Consequence: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.

    -

    4. Permanent Ban

    +

    4. Permanent Ban +

    Community Impact: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.

    Consequence: A permanent ban from any sort of public interaction within the community.

    -

    Attribution

    +

    Attribution +

    This Code of Conduct is adapted from the Contributor Covenant, version 2.1, available at https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.

    Community Impact Guidelines were inspired by Mozilla’s code of conduct enforcement ladder.

    For answers to common questions about this code of conduct, see the FAQ at https://www.contributor-covenant.org/faq. Translations are available at https://www.contributor-covenant.org/translations.

    @@ -123,17 +158,19 @@

    Attribution

    + + + + - - + + diff --git a/v0.1.4/CONTRIBUTING.html b/v0.1.4/CONTRIBUTING.html index 3c31cb10..97970760 100644 --- a/v0.1.4/CONTRIBUTING.html +++ b/v0.1.4/CONTRIBUTING.html @@ -1,8 +1,22 @@ - -Contribution Guidelines • teal.modules.hermes + + + + + + + Skip to contents @@ -18,32 +32,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -59,7 +79,8 @@

    🙏 Thank you for taking the time to contribute!

    Your input is deeply valued, whether an issue, a pull request, or even feedback, regardless of size, content or scope.

    -

    Table of contents

    +

    Table of contents +

    👶 Getting started

    📔 Code of Conduct

    🗃 License

    @@ -70,38 +91,47 @@

    Table of contents❓ Questions

    -

    Getting started

    +

    Getting started +

    Please refer the project documentation for a brief introduction. Please also see other articles within the project documentation for additional information.

    -

    Code of Conduct

    +

    Code of Conduct +

    A Code of Conduct governs this project. Participants and contributors are expected to follow the rules outlined therein.

    -

    License

    +

    License +

    All your contributions will be covered by this project’s license.

    -

    Issues

    +

    Issues +

    We use GitHub to track issues, feature requests, and bugs. Before submitting a new issue, please check if the issue has already been reported. If the issue already exists, please upvote the existing issue 👍.

    For new feature requests, please elaborate on the context and the benefit the feature will have for users, developers, or other relevant personas.

    -

    Pull requests

    +

    Pull requests +

    -

    Github flow

    +

    Github flow +

    This repository uses the Github flow model for collaboration. To submit a pull request:

    -
    1. +
        +

      1. Create a branch.

        Please see the branch naming convention below. If you don’t have write access to this repository, please fork it.

      2. Make changes.

        Make sure your code:

        -
        • passes all checks imposed by GitHub Actions
          • +
            +
          • passes all checks imposed by GitHub Actions
          • is well documented
          • is well tested with unit tests sufficiently covering the changes introduced
            • -
          +
        +

      3. Create a pull request (PR).

        In the pull request description, please link the relevant issue (if any), provide a detailed description of the change, and include any assumptions.

        @@ -115,64 +145,78 @@

        Github flow -

        Branch naming convention

        +

        Branch naming convention +

        Suppose your changes are related to a current issue in the current project; please name your branch as follows: <issue_id>_<short_description>. Please use underscore (_) as a delimiter for word separation. For example, 420_fix_ui_bug would be a suitable branch name if your change is resolving and UI-related bug reported in issue number 420 in the current project.

        If your change affects multiple repositories, please name your branches as follows: <issue_id>_<issue_repo>_<short description>. For example, 69_awesomeproject_fix_spelling_error would reference issue 69 reported in project awesomeproject and aims to resolve one or more spelling errors in multiple (likely related) repositories.

    monorepo and staged.dependencies -

    + +

    Sometimes you might need to change upstream dependent package(s) to be able to submit a meaningful change. We are using staged.dependencies functionality to simulate a monorepo behavior. The dependency configuration is already specified in this project’s staged_dependencies.yaml file. You need to name the feature branches appropriately. This is the only exception from the branch naming convention described above.

    Please refer to the staged.dependencies package documentation for more details.

    -

    Recommended development environment & tools

    +

    Recommended development environment & tools +

    -

    R & package versions

    +

    R & package versions +

    We continuously test our packages against the newest R version along with the most recent dependencies from CRAN and BioConductor. We recommend that your working environment is also set up in the same way. You can find the details about the R version and packages used in the R CMD check GitHub Action execution log - there is a step that prints out the R sessionInfo().

    If you discover bugs on older R versions or with an older set of dependencies, please create the relevant bug reports.

    -

    pre-commit

    +

    +pre-commit +

    We highly recommend that you use the pre-commit tool combined with R hooks for pre-commit to execute some of the checks before committing and pushing your changes.

    Pre-commit hooks are already available in this repository’s .pre-commit-config.yaml file.

    -

    Style guide

    +

    Style guide +

    This repository follows the standard tidyverse style guide and uses lintr for lint checks. Customized lint configurations are available in this repository’s .lintr file.

    -

    Recognition model

    +

    Recognition model +

    As mentioned previously, all contributions are deeply valued and appreciated. While all contribution data is available as part of the repository insights, to recognize a significant contribution and hence add the contributor to the package authors list, the following rules are enforced:

    -
    • Minimum 5% of lines of code authored* (determined by git blame query) OR
      • +
        +
      • Minimum 5% of lines of code authored* (determined by git blame query) OR
      • Being at the top 5 contributors in terms of number of commits OR lines added OR lines removed*
        • -

      *Excluding auto-generated code, including but not limited to roxygen comments or renv.lock files.

      +
    +

    *Excluding auto-generated code, including but not limited to roxygen comments or renv.lock files.

    The package maintainer also reserves the right to adjust the criteria to recognize contributions.

    -

    Questions

    +

    Questions +

    If you have further questions regarding the contribution guidelines, please contact the package/repository maintainer.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/LICENSE-text.html b/v0.1.4/LICENSE-text.html index 57f76ebf..d70093bc 100644 --- a/v0.1.4/LICENSE-text.html +++ b/v0.1.4/LICENSE-text.html @@ -1,8 +1,22 @@ - -License • teal.modules.hermes + + + + + + + Skip to contents @@ -18,32 +32,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,17 +89,19 @@ limitations under the License. - + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/SECURITY.html b/v0.1.4/SECURITY.html index 3482d2c7..47ee515c 100644 --- a/v0.1.4/SECURITY.html +++ b/v0.1.4/SECURITY.html @@ -1,8 +1,22 @@ - -Security Policy • teal.modules.hermes + + + + + + + Skip to contents @@ -18,32 +32,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -57,38 +77,44 @@
    -

    Reporting Security Issues

    +

    Reporting Security Issues +

    If you believe you have found a security vulnerability in any of the repositories in this organization, please report it to us through coordinated disclosure.

    Please do not report security vulnerabilities through public GitHub issues, discussions, or pull requests.

    Instead, please send an email to vulnerability.management[@]roche.com.

    Please include as much of the information listed below as you can to help us better understand and resolve the issue:

    -
    • The type of issue (e.g., buffer overflow, SQL injection, or cross-site scripting)
      • +
        +
      • The type of issue (e.g., buffer overflow, SQL injection, or cross-site scripting)
      • Full paths of source file(s) related to the manifestation of the issue
      • The location of the affected source code (tag/branch/commit or direct URL)
      • Any special configuration required to reproduce the issue
      • Step-by-step instructions to reproduce the issue
      • Proof-of-concept or exploit code (if possible)
      • Impact of the issue, including how an attacker might exploit the issue
        • -

      This information will help us triage your report more quickly.

      +
    +

    This information will help us triage your report more quickly.

    -

    Data Security Standards (DSS)

    +

    Data Security Standards (DSS) +

    Please make sure that while reporting issues in the form a bug, feature, or pull request, all sensitive information such as PII, PHI, and PCI is completely removed from any text and attachments, including pictures and videos.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/authors.html b/v0.1.4/authors.html index 2e8e1f6a..110f9c0a 100644 --- a/v0.1.4/authors.html +++ b/v0.1.4/authors.html @@ -1,8 +1,22 @@ - -Authors and Citation • teal.modules.hermes + + + + + + + Skip to contents @@ -18,32 +32,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -56,7 +76,8 @@

    Authors

    -
    • +
        +

      • Daniel Sabanés Bové. Author, maintainer.

        • @@ -120,7 +141,8 @@

        Authors

        F. Hoffmann-La Roche AG. Copyright holder, funder.

        -
    + +

    Citation

    @@ -139,17 +161,19 @@

    Citation

    }
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/index.html b/v0.1.4/index.html index 5b9245a6..90900083 100644 --- a/v0.1.4/index.html +++ b/v0.1.4/index.html @@ -1,5 +1,4 @@ - - + @@ -43,14 +42,15 @@ Changelog
  • -
    main + +
    + main latest-tag v0.1.6 v0.1.5 -v0.1.4
    • +v0.1.4 + + + + -
    • +
        +
        • -
      +
    + @@ -55,48 +75,70 @@
    -

    teal.modules.hermes 0.1.4

    +

    teal.modules.hermes 0.1.4 +

    -

    teal.modules.hermes 0.1.3

    -
    • Improve the selection of sample variables in the forest module (tm_g_forest_tte) such that only categorical variables can be selected in the first place.
      • +

      teal.modules.hermes 0.1.3 +

      +
        +
      • Improve the selection of sample variables in the forest module (tm_g_forest_tte) such that only categorical variables can be selected in the first place.
      • Added the teal.reporter functionality to all modules.
        • -
      -

      Miscellaneous

      -
      • Added a template to the pkgdown site.
        • +
      +
      +

      Miscellaneous +

      +
        +
      • Added a template to the pkgdown site.
      • Updated package authors.
      • Added the option categorical_only to the sampleVarSpec server module, which allows to only show categorical sample variables for selection.
        • -
      +
    +
    -

    teal.modules.hermes 0.1.2

    -
    • Rewrote modules to use moduleServer and updated call to plot_with_settings_srv after changes in teal.devel.
      • +

      teal.modules.hermes 0.1.2 +

      +
        +
      • Rewrote modules to use moduleServer and updated call to plot_with_settings_srv after changes in teal.devel.
      • Replaced calls to teal::root_modules with teal::modules following deprecation of teal::root_modules.
      • Added basic logging to the modules.
      • Fixed the geneSpecInput so that the hermes app doesn’t fail anymore (on chrome) on an experiment with no genes.
        • -
    + +
    -

    teal.modules.hermes 0.1.1

    +

    teal.modules.hermes 0.1.1 +

    -

    Bug Fixes

    -
    • Updated legend for the PCA plot.
      • +

      Bug Fixes +

      +
        +
      • Updated legend for the PCA plot.
      • Gene selection with more than a few thousand genes no longer hangs the application. This is achieved through a different selection input in the corresponding geneSpec shiny module.
      • Only atomic columns of colData with at least one value can now be selected in the sampleVarSpecModule.
        • -
    + +
    -

    Miscellaneous

    -
    • Updated R version requirement to >= 3.6.
      • +

      Miscellaneous +

      +
        +
      • Updated R version requirement to >= 3.6.
      • Updated sampleVarSpec and geneSpec modules with new icons to remove warnings when using shiny version >= 1.7.
      • Removed dependencies on deprecated packages utils.nest and test.nest.
        • -
    + +
    -

    teal.modules.hermes 0.1.0

    -
    • First release of the teal.modules.hermes package, which contains teal modules for RNA-seq analysis using the hermes package.
      • +

      teal.modules.hermes 0.1.0 +

      +
        +
      • First release of the teal.modules.hermes package, which contains teal modules for RNA-seq analysis using the hermes package.
      • New users should first begin by reading the README.md of the teal.modules.hermes package to become familiar.
        • -
      -

      New Features

      -
      • +
      +
      +

      New Features +

      +
      +
    +
    + + + + - - + + diff --git a/v0.1.4/pull_request_template.html b/v0.1.4/pull_request_template.html index 65e6c763..271f209b 100644 --- a/v0.1.4/pull_request_template.html +++ b/v0.1.4/pull_request_template.html @@ -1,8 +1,22 @@ - -Pull Request • teal.modules.hermes + + + + + + + Skip to contents @@ -18,32 +32,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -60,17 +80,19 @@

    Fixes #nnn

    - + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/reference/adtteSpecInput.html b/v0.1.4/reference/adtteSpecInput.html index 07c907e6..92a6b333 100644 --- a/v0.1.4/reference/adtteSpecInput.html +++ b/v0.1.4/reference/adtteSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for ADTTE Specification — adtteSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,13 +85,16 @@
    -

    Usage

    +

    Usage +

    adtteSpecInput(inputId, label_paramcd = "Select Endpoint")
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -77,30 +102,35 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    adtteSpecServer() for the module server and a complete example.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/reference/adtteSpecServer.html b/v0.1.4/reference/adtteSpecServer.html index 54f7214e..b12b4433 100644 --- a/v0.1.4/reference/adtteSpecServer.html +++ b/v0.1.4/reference/adtteSpecServer.html @@ -1,18 +1,34 @@ - - + + + + + +Module Server for ADTTE Specification — adtteSpecServer • teal.modules.hermes +Module Server for ADTTE Specification — adtteSpecServer • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -28,32 +44,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -75,7 +97,8 @@
    -

    Usage

    +

    Usage +

    adtteSpecServer(
   id,
   datasets,
@@ -91,8 +114,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -113,8 +138,11 @@

    ArgumentsArgumentsArguments -

    Value

    +

    Value +

    -

    List with the following elements:

    • binned_adtte_subset: reactive containing the joined ADTTE and gene data.

      • +

      List with the following elements:

      +
        +

      • binned_adtte_subset: reactive containing the joined ADTTE and gene data.

      • gene_col: reactive containing the string with the column name of the original numeric gene variable.

      • gene_factor: string with the variable name for the binned gene data.

      • time_unit: reactive string with the time unit for the current subset.

        • -
    + +
    -

    See also

    +

    See also +

    adtteSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                datasets) {
   ns <- NS(id)
@@ -256,17 +292,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/assaySpecInput.html b/v0.1.4/reference/assaySpecInput.html index 42786ac3..ee2a7d48 100644 --- a/v0.1.4/reference/assaySpecInput.html +++ b/v0.1.4/reference/assaySpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Assay Specification — assaySpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,13 +85,16 @@
    -

    Usage

    +

    Usage +

    assaySpecInput(inputId, label_assays = "Select Assay")
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -77,30 +102,35 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    assaySpecServer() for the module server and a complete example.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/reference/assaySpecServer.html b/v0.1.4/reference/assaySpecServer.html index 994c3a5e..7e2835d6 100644 --- a/v0.1.4/reference/assaySpecServer.html +++ b/v0.1.4/reference/assaySpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Assay Specification — assaySpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,13 +85,16 @@
    -

    Usage

    +

    Usage +

    assaySpecServer(id, assays, exclude_assays = character())
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -81,20 +106,24 @@

    Arguments -

    Value

    +

    Value +

    The chosen assay as a reactive string.

    -

    See also

    +

    See also +

    assaySpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                datasets) {
   ns <- NS(id)
@@ -156,17 +185,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/assert_adtte_vars.html b/v0.1.4/reference/assert_adtte_vars.html index 6bd3f238..989167bf 100644 --- a/v0.1.4/reference/assert_adtte_vars.html +++ b/v0.1.4/reference/assert_adtte_vars.html @@ -1,10 +1,26 @@ - -Check for ADTTE Variables — assert_adtte_vars • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,38 +85,46 @@
    -

    Usage

    +

    Usage +

    assert_adtte_vars(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    -
    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    assert_adtte_vars(list(aval = "AV", is_event = "EV", paramcd = "PC", usubjid = "ID", avalu = "u"))
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/reference/assert_summary_funs.html b/v0.1.4/reference/assert_summary_funs.html index 842b8935..d642b7ff 100644 --- a/v0.1.4/reference/assert_summary_funs.html +++ b/v0.1.4/reference/assert_summary_funs.html @@ -1,10 +1,26 @@ - -Check for List of Summary Functions — assert_summary_funs • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,13 +85,16 @@
    -

    Usage

    +

    Usage +

    assert_summary_funs(x, null.ok = FALSE)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    @@ -77,29 +102,34 @@

    Arguments -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    assert_summary_funs(list(mean = colMeans, raw = NULL), null.ok = TRUE)
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/reference/assertion_arguments.html b/v0.1.4/reference/assertion_arguments.html index 4bf2c470..a41c7735 100644 --- a/v0.1.4/reference/assertion_arguments.html +++ b/v0.1.4/reference/assertion_arguments.html @@ -1,10 +1,26 @@ - -Standard Assertion Arguments — assertion_arguments • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -64,8 +86,10 @@
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    @@ -92,19 +116,22 @@

    Argumentscheckmate::vname().

    -

    + + - + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/reference/assertions.html b/v0.1.4/reference/assertions.html index 10b1755a..54dc3fec 100644 --- a/v0.1.4/reference/assertions.html +++ b/v0.1.4/reference/assertions.html @@ -1,14 +1,30 @@ - - + + + + + +Additional Assertions for checkmate — assertions • teal.modules.hermes +Additional Assertions for checkmate — assertions • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,39 +40,46 @@ + - + + -
    • +
        +
        • -
      +
    +
    -

    Additional Assertions for checkmate

    +

    Additional Assertions for checkmate +

    Source: R/checkmate.R
    assertions.Rd
    @@ -70,32 +93,39 @@
    -

    Value

    +

    Value +

    -

    Depending on the function prefix.

    • assert_ functions return the object invisibly if successful, and otherwise +

      Depending on the function prefix.

      +
        +

      • assert_ functions return the object invisibly if successful, and otherwise throw an error message.

      • check_ functions return TRUE if successful, otherwise a string with the error message.

      • test_ functions just return TRUE or FALSE.

        • -
    + +
    -

    See also

    +

    See also +

    assert_tag(), assert_reactive(), assert_summary_funs(), assert_adtte_vars()

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/reference/check_reactive.html b/v0.1.4/reference/check_reactive.html index e87970d5..1186a573 100644 --- a/v0.1.4/reference/check_reactive.html +++ b/v0.1.4/reference/check_reactive.html @@ -1,10 +1,26 @@ - -Check for Reactive Input — check_reactive • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    check_reactive(x)
 
 assert_reactive(x, .var.name = checkmate::vname(x), add = NULL)
@@ -72,8 +95,10 @@ 
    Usage
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    @@ -86,14 +111,17 @@

    Argumentscheckmate::AssertCollection.

    -

    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    check_reactive("bla")
 #> [1] FALSE
 check_reactive(reactive("bla"))
@@ -101,17 +129,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/check_tag.html b/v0.1.4/reference/check_tag.html index 071d0ec3..8f1d4a05 100644 --- a/v0.1.4/reference/check_tag.html +++ b/v0.1.4/reference/check_tag.html @@ -1,10 +1,26 @@ - -Check for Shiny Tag — check_tag • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    check_tag(x, null.ok = FALSE)
 
 assert_tag(x, null.ok = FALSE, .var.name = checkmate::vname(x), add = NULL)
@@ -74,8 +97,10 @@ 
    Usage
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    @@ -102,14 +127,17 @@

    Argumentscheckmate::vname().

    -

    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    check_tag("bla")
 #> [1] "Must be a 'shiny.tag' or NULL"
 check_tag(NULL, null.ok = TRUE)
@@ -117,17 +145,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/experimentSpecInput.html b/v0.1.4/reference/experimentSpecInput.html index 3fa62f6d..4ca91b81 100644 --- a/v0.1.4/reference/experimentSpecInput.html +++ b/v0.1.4/reference/experimentSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Experiment Specification — experimentSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    experimentSpecInput(
   inputId,
   datasets,
@@ -73,8 +96,10 @@ 
    Usage
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -93,30 +118,35 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    experimentSpecServer() for the module server and a complete example.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/reference/experimentSpecServer.html b/v0.1.4/reference/experimentSpecServer.html index 10e1ec51..cfa6be65 100644 --- a/v0.1.4/reference/experimentSpecServer.html +++ b/v0.1.4/reference/experimentSpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Experiment Specification — experimentSpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    experimentSpecServer(
   id,
   datasets,
@@ -75,8 +98,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -106,23 +131,30 @@

    Arguments -

    Value

    +

    Value +

    -

    List with the following reactive objects:

    • data: the hermes::AnyHermesData experiment.

      • +

      List with the following reactive objects:

      +
        +

      • data: the hermes::AnyHermesData experiment.

      • name: the name of the experiment as selected by the user.

      • genes: a data.frame with the genes in data, with columns id and name.

      • assays: the names of the assays in data.

        • -
    + +
    -

    See also

    +

    See also +

    experimentSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                datasets,
                mae_name) {
@@ -202,17 +234,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/function_arguments.html b/v0.1.4/reference/function_arguments.html index 715e2ed3..dc0eebac 100644 --- a/v0.1.4/reference/function_arguments.html +++ b/v0.1.4/reference/function_arguments.html @@ -1,10 +1,26 @@ - -Standard Function Arguments — function_arguments • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -64,8 +86,10 @@
    -

    Arguments

    -
    adtte
    +

    Arguments +

    +
    +
    adtte

    (data frame)
    an adtte dataset.

    @@ -93,19 +117,22 @@

    Arguments

    teal.modules.hermes is a part of the NEST and pharmaverse.

    - + + - - + + diff --git a/v0.1.4/reference/geneSpecInput.html b/v0.1.4/reference/geneSpecInput.html index 61bc5a3f..ab402418 100644 --- a/v0.1.4/reference/geneSpecInput.html +++ b/v0.1.4/reference/geneSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Gene Signature Specification — geneSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    geneSpecInput(
   inputId,
   funs,
@@ -80,8 +103,10 @@ 
    Usage
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -123,20 +148,24 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    geneSpecServer() for the module server and a complete example.

    -

    Examples

    +

    Examples +

    geneSpecInput("my_genes", list(mean = colMeans), label_funs = "Please select function")
 #> <div class="row">
 #>   <div class="col-sm-8">
@@ -202,17 +231,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/geneSpecServer.html b/v0.1.4/reference/geneSpecServer.html index 9750a512..0ce1a508 100644 --- a/v0.1.4/reference/geneSpecServer.html +++ b/v0.1.4/reference/geneSpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Gene Signature Specification — geneSpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    geneSpecServer(
   id,
   funs,
@@ -75,8 +98,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -97,21 +122,25 @@

    Arguments -

    Value

    +

    Value +

    Reactive hermes::GeneSpec which can be used as input for the relevant hermes functions.

    -

    See also

    +

    See also +

    geneSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                datasets,
                funs) {
@@ -183,17 +212,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/h_assign_to_group_list.html b/v0.1.4/reference/h_assign_to_group_list.html index c479c3bb..3954911c 100644 --- a/v0.1.4/reference/h_assign_to_group_list.html +++ b/v0.1.4/reference/h_assign_to_group_list.html @@ -1,12 +1,28 @@ - - + + + + + +Helper Function For Group List Creation — h_assign_to_group_list • teal.modules.hermes +Helper Function For Group List Creation — h_assign_to_group_list • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,25 +88,31 @@
    -

    Usage

    +

    Usage +

    h_assign_to_group_list(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (named list of character)
    input assignment list.

    -
    + +
    -

    Value

    +

    Value +

    A combination list.

    -

    Examples

    +

    Examples +

    assign_list <- list(
   "ASIAN" = "1",
   "BLACK OR AFRICAN AMERICAN" = "1",
@@ -102,17 +130,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/h_collapse_levels.html b/v0.1.4/reference/h_collapse_levels.html index 6395d78d..1ccd7197 100644 --- a/v0.1.4/reference/h_collapse_levels.html +++ b/v0.1.4/reference/h_collapse_levels.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function for Collapsing of Factor Levels — h_collapse_levels • teal.modules.hermes +Helper Function for Collapsing of Factor Levels — h_collapse_levels • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,32 +40,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,13 +91,16 @@
    -

    Usage

    +

    Usage +

    h_collapse_levels(x, group_list)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (factor)
    original factor.

    @@ -83,16 +108,19 @@

    Arguments -

    Value

    +

    Value +

    The transformed factor x with new levels.

    -

    Examples

    +

    Examples +

    set.seed(123)
 x <- factor(sample(
   c("ASIAN", "BLACK OR AFRICAN AMERICAN", "MULTIPLE", "UNKNOWN", "WHITE"),
@@ -109,17 +137,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/h_extract_words.html b/v0.1.4/reference/h_extract_words.html index 2b5b2161..ec0ae499 100644 --- a/v0.1.4/reference/h_extract_words.html +++ b/v0.1.4/reference/h_extract_words.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Extract Words — h_extract_words • teal.modules.hermes +Helper Function to Extract Words — h_extract_words • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,32 +40,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,25 +91,31 @@
    -

    Usage

    +

    Usage +

    h_extract_words(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (string)
    input.

    -
    + +
    -

    Value

    +

    Value +

    Character vector with the extracted words.

    -

    Examples

    +

    Examples +

    h_extract_words("a, b, , c, 234; 34562 - GeneID:bla")
 #> [1] "a"          "b"          "c"          "234"        "34562"     
 #> [6] "GeneID:bla"
@@ -96,17 +124,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/h_gene_data.html b/v0.1.4/reference/h_gene_data.html index 292fd585..1671adab 100644 --- a/v0.1.4/reference/h_gene_data.html +++ b/v0.1.4/reference/h_gene_data.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Format Gene Choices — h_gene_data • teal.modules.hermes +Helper Function to Format Gene Choices — h_gene_data • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,32 +40,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,13 +91,16 @@
    -

    Usage

    +

    Usage +

    h_gene_data(object, name_annotation)
    -

    Arguments

    -
    object
    +

    Arguments +

    +
    +
    object

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    @@ -84,23 +109,27 @@

    Arguments -

    Value

    +

    Value +

    A data.frame with id and name columns containing all genes from object.

    -

    Details

    +

    Details +

    Note that missing names or names that only contain whitespace are replaced by empty strings for consistency and better labeling in the UI downstream

    -

    Examples

    +

    Examples +

    object <- hermes::hermes_data[1:10, ]
 h_gene_data(object, "symbol")
 #>                  id         name
@@ -117,17 +146,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/h_km_mae_to_adtte.html b/v0.1.4/reference/h_km_mae_to_adtte.html index 0ab86507..2af632da 100644 --- a/v0.1.4/reference/h_km_mae_to_adtte.html +++ b/v0.1.4/reference/h_km_mae_to_adtte.html @@ -1,10 +1,26 @@ - -Data Preprocessing for ADTTE Module — h_km_mae_to_adtte • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    h_km_mae_to_adtte(
   adtte,
   mae,
@@ -75,8 +98,10 @@ 
    Usage
    -

    Arguments

    -
    adtte
    +

    Arguments +

    +
    +
    adtte

    (data frame)
    an adtte dataset.

    @@ -100,9 +125,11 @@

    Arguments -

    Value

    +

    Value +

    A data frame containing all columns/rows from adtte that match @@ -111,13 +138,15 @@

    Value

    -

    Note

    +

    Note +

    The final gene column names can start with a different string than the original gene IDs (or labels), in particular white space and colons are removed.

    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 adtte <- scda::synthetic_cdisc_data("rcd_2021_07_07")$adtte %>%
   dplyr::mutate(CNSR = as.logical(CNSR))
@@ -143,17 +172,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/h_order_genes.html b/v0.1.4/reference/h_order_genes.html index 9b689c48..2b7b4dab 100644 --- a/v0.1.4/reference/h_order_genes.html +++ b/v0.1.4/reference/h_order_genes.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Order Gene Choices — h_order_genes • teal.modules.hermes +Helper Function to Order Gene Choices — h_order_genes • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,32 +40,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,26 +91,32 @@
    -

    Usage

    +

    Usage +

    h_order_genes(genes)
    -

    Arguments

    -
    genes
    +

    Arguments +

    +
    +
    genes

    (data.frame)
    containing id and name columns of the gene choices. Note that no missing values are allowed.

    -
    + +
    -

    Value

    +

    Value +

    The ordered data.frame.

    -

    Examples

    +

    Examples +

    genes <- data.frame(
   id = c("7", "1", "2", "345346", "0"),
   name = c("e", "", "c", "", "a")
@@ -103,17 +131,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/h_parse_genes.html b/v0.1.4/reference/h_parse_genes.html index fb913c10..19f0bfe2 100644 --- a/v0.1.4/reference/h_parse_genes.html +++ b/v0.1.4/reference/h_parse_genes.html @@ -1,12 +1,28 @@ - - + + + + + +Helper Function to Parse Genes — h_parse_genes • teal.modules.hermes +Helper Function to Parse Genes — h_parse_genes • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,13 +88,16 @@
    -

    Usage

    +

    Usage +

    h_parse_genes(words, choices)
    -

    Arguments

    -
    words
    +

    Arguments +

    +
    +
    words

    (character)
    containing gene IDs or names.

    @@ -80,16 +105,19 @@

    Arguments -

    Value

    +

    Value +

    The subset of choices which matches words in ID or name.

    -

    Examples

    +

    Examples +

    h_parse_genes(
   c("a", "2535"),
   data.frame(id = as.character(2533:2537), name = letters[1:5])
@@ -100,17 +128,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/h_update_gene_selection.html b/v0.1.4/reference/h_update_gene_selection.html index dbb32ce7..ce91e9fe 100644 --- a/v0.1.4/reference/h_update_gene_selection.html +++ b/v0.1.4/reference/h_update_gene_selection.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Update Gene Selection — h_update_gene_selection • teal.modules.hermes +Helper Function to Update Gene Selection — h_update_gene_selection • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,32 +40,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,13 +91,16 @@
    -

    Usage

    +

    Usage +

    h_update_gene_selection(session, inputId, selected, choices)
    -

    Arguments

    -
    session
    +

    Arguments +

    +
    +
    session

    (ShinySession)
    the session object.

    @@ -92,20 +117,23 @@

    Arguments

    + + + + - - + + diff --git a/v0.1.4/reference/heatmap_plot.html b/v0.1.4/reference/heatmap_plot.html index 846f3821..e6aeadb2 100644 --- a/v0.1.4/reference/heatmap_plot.html +++ b/v0.1.4/reference/heatmap_plot.html @@ -1,10 +1,26 @@ - -Correlation Heatmap Plot — heatmap_plot • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,29 +85,35 @@
    -

    Usage

    +

    Usage +

    heatmap_plot(object, assay_name)
    -

    Arguments

    -
    object
    +

    Arguments +

    +
    +
    object

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    assay_name

    (string)
    the assay to define the groups.

    -
    + +
    -

    Value

    +

    Value +

    Plot to be displayed in the teal app.

    -

    Examples

    +

    Examples +

    library(hermes)
 #> Loading required package: ggfortify
 #> Loading required package: SummarizedExperiment
@@ -163,17 +191,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/include_css_files.html b/v0.1.4/reference/include_css_files.html index 8a66ccc3..bb68eca9 100644 --- a/v0.1.4/reference/include_css_files.html +++ b/v0.1.4/reference/include_css_files.html @@ -1,12 +1,28 @@ - - + + + + + +Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.modules.hermes +Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,35 +88,42 @@
    -

    Usage

    +

    Usage +

    include_css_files(pattern = "*")
    -

    Arguments

    -
    pattern
    +

    Arguments +

    +
    +
    pattern

    (character) pattern of files to be included

    -
    + +
    -

    Value

    +

    Value +

    HTML code that includes CSS files

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/reference/include_js_files.html b/v0.1.4/reference/include_js_files.html index c60fd549..2c5ffcdb 100644 --- a/v0.1.4/reference/include_js_files.html +++ b/v0.1.4/reference/include_js_files.html @@ -1,12 +1,28 @@ - - + + + + + +Include JS files from /inst/js/ package directory to application header — include_js_files • teal.modules.hermes +Include JS files from /inst/js/ package directory to application header — include_js_files • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,39 +88,46 @@
    -

    Usage

    +

    Usage +

    include_js_files(pattern = "*")
    -

    Arguments

    -
    pattern
    +

    Arguments +

    +
    +
    pattern

    (character) pattern of files to be included, passed to system.file

    except

    (character) vector of basename filenames to be excluded

    -
    + +
    -

    Value

    +

    Value +

    HTML code that includes JS files

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/reference/index.html b/v0.1.4/reference/index.html index 5bf1d6cd..cb7c0927 100644 --- a/v0.1.4/reference/index.html +++ b/v0.1.4/reference/index.html @@ -1,8 +1,22 @@ - -Function reference • teal.modules.hermes + + + + + + + Skip to contents @@ -18,32 +32,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -54,280 +74,377 @@
    -

    Package

    +

    Package +

    -
    +
    +
    -
    +
    +
    teal.modules.hermes teal.modules.hermes-package
    -
    teal.modules.hermes Package
    -
    -

    Utility Functions

    +
    +teal.modules.hermes Package
    + +
    +
    +

    Utility Functions +

    -
    +
    +
    -
    +
    +
    h_assign_to_group_list()
    Helper Function For Group List Creation
    -
    +
    +
    +
    h_collapse_levels()
    Helper Function for Collapsing of Factor Levels
    -
    +
    +
    +
    h_extract_words()
    Helper Function to Extract Words
    -
    +
    +
    +
    h_gene_data()
    Helper Function to Format Gene Choices
    -
    +
    +
    +
    h_km_mae_to_adtte()
    Data Preprocessing for ADTTE Module
    -
    +
    +
    +
    h_order_genes()
    Helper Function to Order Gene Choices
    -
    +
    +
    +
    h_parse_genes()
    Helper Function to Parse Genes
    -
    +
    +
    +
    h_update_gene_selection()
    Helper Function to Update Gene Selection
    -
    +
    +
    +
    is_blank()
    Checking for Empty String
    -
    -

    Shiny Modules

    + +
    +
    +

    Shiny Modules +

    -
    +
    +
    -
    +
    +
    adtteSpecInput()
    Module Input for ADTTE Specification
    -
    +
    +
    +
    adtteSpecServer()
    Module Server for ADTTE Specification
    -
    +
    +
    +
    assaySpecInput()
    Module Input for Assay Specification
    -
    +
    +
    +
    assaySpecServer()
    Module Server for Assay Specification
    -
    +
    +
    +
    experimentSpecInput()
    Module Input for Experiment Specification
    -
    +
    +
    +
    experimentSpecServer()
    Module Server for Experiment Specification
    -
    +
    +
    +
    geneSpecInput()
    Module Input for Gene Signature Specification
    -
    +
    +
    +
    geneSpecServer()
    Module Server for Gene Signature Specification
    -
    +
    +
    +
    sampleVarSpecInput()
    Module Input for Sample Variable Specification
    -
    +
    +
    +
    sampleVarSpecServer()
    Module Server for Sample Variable Specification
    -
    +
    +
    +
    multiSampleVarSpecServer()
    Module Server for Specification of Multiple Sample Variables
    -
    -

    Teal Module Functions

    + +
    +
    +

    Teal Module Functions +

    -
    +
    +
    -
    +
    +
    tm_g_barplot() ui_g_barplot() srv_g_barplot() sample_tm_g_barplot()
    Teal Module for RNA-seq Barplot
    -
    +
    +
    +
    tm_g_boxplot() ui_g_boxplot() srv_g_boxplot() sample_tm_g_boxplot()
    Teal Module for RNA-seq Boxplot
    -
    +
    +
    +
    tm_g_forest_tte() ui_g_forest_tte() srv_g_forest_tte() sample_tm_g_forest_tte()
    Teal Module for Survival Forest Plot
    -
    +
    +
    +
    tm_g_km() ui_g_km() srv_g_km() sample_tm_g_km()
    Teal Module for Kaplan-Meier Plot
    -
    +
    +
    +
    tm_g_pca() ui_g_pca() srv_g_pca() sample_tm_g_pca()
    Teal Module for PCA Analysis
    -
    +
    +
    +
    tm_g_quality() ui_g_quality() srv_g_quality() sample_tm_g_quality()
    Teal Module for RNA-seq Quality Control
    -
    +
    +
    +
    tm_g_scatterplot() ui_g_scatterplot() srv_g_scatterplot() sample_tm_g_scatterplot()
    Teal Module for RNA-seq Scatterplot
    -
    +
    +
    +
    tm_g_volcanoplot() ui_g_volcanoplot() srv_g_volcanoplot() sample_tm_g_volcanoplot()
    Teal Module for RNA-seq Volcano Plot
    -
    -

    Graph Functions

    + +
    +
    +

    Graph Functions +

    -
    +
    +
    -
    +
    +
    heatmap_plot()
    Correlation Heatmap Plot
    -
    +
    +
    +
    top_gene_plot()
    Most Expressed Genes Plot
    -
    -

    Assertions

    + +
    +
    +

    Assertions +

    -
    +
    +
    -
    +
    +
    assert_adtte_vars()
    Check for ADTTE Variables
    -
    +
    +
    +
    check_reactive() assert_reactive() test_reactive()
    Check for Reactive Input
    -
    +
    +
    +
    assert_summary_funs()
    Check for List of Summary Functions
    -
    +
    +
    +
    check_tag() assert_tag() test_tag() expect_tag()
    Check for Shiny Tag
    -
    -

    Validations

    + +
    +
    +

    Validations +

    -
    +
    +
    -
    +
    +
    validate_gene_spec()
    Validation of Gene Specification
    -
    +
    +
    +
    validate_n_levels()
    Validation of Number of Levels
    -
    + + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/reference/is_blank.html b/v0.1.4/reference/is_blank.html index 833d8166..cf4849ba 100644 --- a/v0.1.4/reference/is_blank.html +++ b/v0.1.4/reference/is_blank.html @@ -1,12 +1,28 @@ - - + + + + + +Checking for Empty String — is_blank • teal.modules.hermes +Checking for Empty String — is_blank • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,25 +88,31 @@
    -

    Usage

    +

    Usage +

    is_blank(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    object to check.

    -
    + +
    -

    Value

    +

    Value +

    Flag whether x is identical to an empty string, i.e. "".

    -

    Examples

    +

    Examples +

    is_blank("")
 #> [1] TRUE
 is_blank(" ")
@@ -92,17 +120,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/module_arguments.html b/v0.1.4/reference/module_arguments.html index 8b81c4b7..6ec777cb 100644 --- a/v0.1.4/reference/module_arguments.html +++ b/v0.1.4/reference/module_arguments.html @@ -1,10 +1,26 @@ - -Standard Module Arguments — module_arguments • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -64,8 +86,10 @@
    -

    Arguments

    -
    datasets
    +

    Arguments +

    +
    +
    datasets

    (Datasets)
    teal specific argument which is automatically passed to the UI and server functions, holding all the data sets provided in the app initialization.

    @@ -87,8 +111,11 @@

    ArgumentsArgumentsArguments

    teal.modules.hermes is a part of the NEST and pharmaverse.

    - + + - - + + diff --git a/v0.1.4/reference/multiSampleVarSpecServer.html b/v0.1.4/reference/multiSampleVarSpecServer.html index 05de624b..5fb08337 100644 --- a/v0.1.4/reference/multiSampleVarSpecServer.html +++ b/v0.1.4/reference/multiSampleVarSpecServer.html @@ -1,12 +1,28 @@ - - + + + + + +Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer • teal.modules.hermes +Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,13 +88,16 @@
    -

    Usage

    +

    Usage +

    multiSampleVarSpecServer(inputIds, original_data, ...)
    -

    Arguments

    -
    inputIds
    +

    Arguments +

    +
    +
    inputIds

    (character)
    multiple input IDs corresponding to the different sample variables specified in the UI function.

    @@ -90,9 +115,11 @@

    Arguments -

    Value

    +

    Value +

    List with the final transformed experiment_data reactive and a @@ -101,21 +128,24 @@

    Value

    -

    Examples

    +

    Examples +

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/reference/sampleVarSpecInput.html b/v0.1.4/reference/sampleVarSpecInput.html index 36c9b8ec..8c645963 100644 --- a/v0.1.4/reference/sampleVarSpecInput.html +++ b/v0.1.4/reference/sampleVarSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Sample Variable Specification — sampleVarSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    sampleVarSpecInput(
   inputId,
   label_vars = "Select sample variable",
@@ -72,8 +95,10 @@ 
    Usage
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -85,20 +110,24 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    sampleVarSpecServer() for the module server and a complete example.

    -

    Examples

    +

    Examples +

    sampleVarSpecInput("my_vars", label_vars = "Select faceting variable")
 #> <div class="row">
 #>   <div class="col-sm-8">
@@ -121,17 +150,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/sampleVarSpecServer.html b/v0.1.4/reference/sampleVarSpecServer.html index 3240c10e..7fde500e 100644 --- a/v0.1.4/reference/sampleVarSpecServer.html +++ b/v0.1.4/reference/sampleVarSpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Sample Variable Specification — sampleVarSpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    sampleVarSpecServer(
   id,
   experiment_name,
@@ -78,8 +101,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -122,27 +147,32 @@

    Arguments -

    Value

    +

    Value +

    Reactive SummarizedExperiment::SummarizedExperiment which can be used as input for the relevant hermes functions.

    -

    Note

    +

    Note +

    Only atomic columns (e.g. not DataFrame columns) of the colData which are not completely missing (NA) will be shown for selection. If num_levels is specified then only factor columns will be available.

    -

    See also

    +

    See also +

    sampleVarSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                datasets) {
   ns <- NS(id)
@@ -208,17 +238,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/teal.modules.hermes-package.html b/v0.1.4/reference/teal.modules.hermes-package.html index bdb847c7..2d579b55 100644 --- a/v0.1.4/reference/teal.modules.hermes-package.html +++ b/v0.1.4/reference/teal.modules.hermes-package.html @@ -1,10 +1,26 @@ - -teal.modules.hermes Package — teal.modules.hermes-package • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,39 +36,46 @@ + - + + -
    • +
        +
        • -
      +
    +
    -

    teal.modules.hermes Package

    +

    +teal.modules.hermes Package

    Source: R/package.R
    teal.modules.hermes-package.Rd
    @@ -64,15 +87,23 @@
    -

    See also

    -

    Useful links:

    +
    -

    Author

    +

    Author +

    Maintainer: Daniel Sabanés Bové daniel.sabanes_bove@roche.com

    -

    Authors:

    • Nikolas Burkoff

      • +

      Authors:

      +
        +

      • Nikolas Burkoff

      • Dinakar Kulkarni

      • Konrad Pagacz

      • Namrata Bhatia

        • @@ -82,25 +113,31 @@

        Author<

      • Stefanie Bienert

      • Haocheng Li

      • Lyndsee Midori Zhang

        • -

      Other contributors:

      • Sorin Voicu [contributor]

        • +
      +

      Other contributors:

      +
        +

      • Sorin Voicu [contributor]

      • Benoit Falquet [contributor]

      • Mahmoud Hallal [contributor]

      • Tim Treis [contributor]

      • F. Hoffmann-La Roche AG [copyright holder, funder]

        • -
    + +
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/reference/tm_g_barplot.html b/v0.1.4/reference/tm_g_barplot.html index ad54bba0..da7b1453 100644 --- a/v0.1.4/reference/tm_g_barplot.html +++ b/v0.1.4/reference/tm_g_barplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Barplot — tm_g_barplot • teal.modules.hermes +Teal Module for RNA-seq Barplot — tm_g_barplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    tm_g_barplot(
   label,
   mae_name,
@@ -85,8 +108,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -131,23 +156,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_barplot(): sets up the user interface.

      • +
        +

      • ui_g_barplot(): sets up the user interface.

      • srv_g_barplot(): sets up the server with reactive graph.

      • sample_tm_g_barplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -172,17 +203,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/tm_g_boxplot.html b/v0.1.4/reference/tm_g_boxplot.html index 6759bae1..3ff812c2 100644 --- a/v0.1.4/reference/tm_g_boxplot.html +++ b/v0.1.4/reference/tm_g_boxplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Boxplot — tm_g_boxplot • teal.modules.hermes +Teal Module for RNA-seq Boxplot — tm_g_boxplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    tm_g_boxplot(
   label,
   mae_name,
@@ -85,8 +108,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -131,23 +156,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_boxplot(): sets up the user interface.

      • +
        +

      • ui_g_boxplot(): sets up the user interface.

      • srv_g_boxplot(): sets up the server with reactive graph.

      • sample_tm_g_boxplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -172,17 +203,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/tm_g_forest_tte.html b/v0.1.4/reference/tm_g_forest_tte.html index d7d80f56..e945d2c9 100644 --- a/v0.1.4/reference/tm_g_forest_tte.html +++ b/v0.1.4/reference/tm_g_forest_tte.html @@ -1,10 +1,26 @@ - -Teal Module for Survival Forest Plot — tm_g_forest_tte • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,7 +85,8 @@
    -

    Usage

    +

    Usage +

    tm_g_forest_tte(
   label,
   adtte_name,
@@ -106,8 +129,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -123,8 +148,11 @@

    ArgumentsArgumentsArguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_forest_tte(): sets up the user interface.

      • +
        +

      • ui_g_forest_tte(): sets up the user interface.

      • srv_g_forest_tte(): sets up the server with reactive graph.

      • sample_tm_g_forest_tte(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 adtte <- scda::synthetic_cdisc_data("rcd_2021_07_07")$adtte %>%
   dplyr::mutate(is_event = (.data$CNSR == 0))
@@ -232,17 +267,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/tm_g_km.html b/v0.1.4/reference/tm_g_km.html index c459ab3d..a31c0357 100644 --- a/v0.1.4/reference/tm_g_km.html +++ b/v0.1.4/reference/tm_g_km.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for Kaplan-Meier Plot — tm_g_km • teal.modules.hermes +Teal Module for Kaplan-Meier Plot — tm_g_km • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    tm_g_km(
   label,
   adtte_name,
@@ -105,8 +128,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -122,8 +147,11 @@

    ArgumentsArgumentsArguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_km(): sets up the user interface.

      • +
        +

      • ui_g_km(): sets up the user interface.

      • srv_g_km(): sets up the user interface.

      • sample_tm_g_km(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 adtte <- scda::synthetic_cdisc_data("rcd_2021_07_07")$adtte %>%
   dplyr::mutate(is_event = (.data$CNSR == 0))
@@ -225,17 +260,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/tm_g_pca.html b/v0.1.4/reference/tm_g_pca.html index 175385e6..68e2b7cd 100644 --- a/v0.1.4/reference/tm_g_pca.html +++ b/v0.1.4/reference/tm_g_pca.html @@ -1,14 +1,30 @@ - - + + + + + +Teal Module for PCA Analysis — tm_g_pca • teal.modules.hermes +Teal Module for PCA Analysis — tm_g_pca • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,32 +40,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_pca(
   label,
   mae_name,
@@ -86,8 +109,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -126,23 +151,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_pca(): sets up the user interface.

      • +
        +

      • ui_g_pca(): sets up the user interface.

      • srv_g_pca(): sets up the server with reactive graph.

      • sample_tm_g_pca(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -167,17 +198,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/tm_g_quality.html b/v0.1.4/reference/tm_g_quality.html index 811ca87e..c0880a97 100644 --- a/v0.1.4/reference/tm_g_quality.html +++ b/v0.1.4/reference/tm_g_quality.html @@ -1,14 +1,30 @@ - - + + + + + +Teal Module for RNA-seq Quality Control — tm_g_quality • teal.modules.hermes +Teal Module for RNA-seq Quality Control — tm_g_quality • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,32 +40,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_quality(
   label,
   mae_name,
@@ -86,8 +109,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -126,23 +151,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_quality(): sets up the user interface.

      • +
        +

      • ui_g_quality(): sets up the user interface.

      • srv_g_quality(): sets up the server with reactive graphs.

      • sample_tm_g_quality(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -166,17 +197,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/tm_g_scatterplot.html b/v0.1.4/reference/tm_g_scatterplot.html index cf9471e1..37d0017f 100644 --- a/v0.1.4/reference/tm_g_scatterplot.html +++ b/v0.1.4/reference/tm_g_scatterplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Scatterplot — tm_g_scatterplot • teal.modules.hermes +Teal Module for RNA-seq Scatterplot — tm_g_scatterplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    tm_g_scatterplot(
   label,
   mae_name,
@@ -92,8 +115,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -138,23 +163,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_scatterplot(): sets up the user interface.

      • +
        +

      • ui_g_scatterplot(): sets up the user interface.

      • srv_g_scatterplot(): sets up the server with reactive graph.

      • sample_tm_g_scatterplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -179,17 +210,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/tm_g_volcanoplot.html b/v0.1.4/reference/tm_g_volcanoplot.html index 5ecbae1b..82628dd7 100644 --- a/v0.1.4/reference/tm_g_volcanoplot.html +++ b/v0.1.4/reference/tm_g_volcanoplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot • teal.modules.hermes +Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    tm_g_volcanoplot(
   label,
   mae_name,
@@ -83,8 +106,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -123,23 +148,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_volcanoplot(): sets up the user interface.

      • +
        +

      • ui_g_volcanoplot(): sets up the user interface.

      • srv_g_volcanoplot(): sets up the server with reactive graph.

      • sample_tm_g_volcanoplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -164,17 +195,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.4/reference/top_gene_plot.html b/v0.1.4/reference/top_gene_plot.html index de1e78c6..10c27efc 100644 --- a/v0.1.4/reference/top_gene_plot.html +++ b/v0.1.4/reference/top_gene_plot.html @@ -1,10 +1,26 @@ - -Most Expressed Genes Plot — top_gene_plot • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,32 +36,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,46 +85,54 @@
    -

    Usage

    +

    Usage +

    top_gene_plot(object, assay_name)
    -

    Arguments

    -
    object
    +

    Arguments +

    +
    +
    object

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    assay_name

    (string)
    the assay to define the groups.

    -
    + +
    -

    Value

    +

    Value +

    Plot to be displayed in the teal app.

    -

    Examples

    +

    Examples +

    library(hermes)
 object <- HermesData(summarized_experiment)
 result <- top_gene_plot(object, assay_name = "counts")
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/reference/validate_gene_spec.html b/v0.1.4/reference/validate_gene_spec.html index 3e1f4a4f..241ae4b8 100644 --- a/v0.1.4/reference/validate_gene_spec.html +++ b/v0.1.4/reference/validate_gene_spec.html @@ -1,12 +1,28 @@ - - + + + + + +Validation of Gene Specification — validate_gene_spec • teal.modules.hermes +Validation of Gene Specification — validate_gene_spec • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,33 +88,39 @@
    -

    Usage

    +

    Usage +

    validate_gene_spec(gene_spec, gene_choices)
    -

    Arguments

    -
    gene_spec
    +

    Arguments +

    +
    +
    gene_spec

    (GeneSpec)
    gene specification.

    gene_choices

    (character)
    all possible gene choices.

    -
    + + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.4/reference/validate_n_levels.html b/v0.1.4/reference/validate_n_levels.html index deeda343..a538d35c 100644 --- a/v0.1.4/reference/validate_n_levels.html +++ b/v0.1.4/reference/validate_n_levels.html @@ -1,12 +1,28 @@ - - + + + + + +Validation of Number of Levels — validate_n_levels • teal.modules.hermes +Validation of Number of Levels — validate_n_levels • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,32 +38,38 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,13 +88,16 @@
    -

    Usage

    +

    Usage +

    validate_n_levels(x, name, n_levels)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (factor)
    factor to validate.

    @@ -83,20 +108,23 @@

    Arguments

    + + + + - - + + diff --git a/v0.1.5/404.html b/v0.1.5/404.html index accf9c64..549a2e42 100644 --- a/v0.1.5/404.html +++ b/v0.1.5/404.html @@ -1,5 +1,4 @@ - - + @@ -44,14 +43,15 @@ Changelog
  • -
    main + +
    + main latest-tag v0.1.6 v0.1.5 -v0.1.4
    • +v0.1.4 + + + + -
    • +
        +
        • -
      +
    + @@ -60,65 +80,80 @@
    -

    Our Pledge

    +

    Our Pledge +

    We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.

    We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.

    -

    Our Standards

    +

    Our Standards +

    Examples of behavior that contributes to a positive environment for our community include:

    -
    • Demonstrating empathy and kindness toward other people
      • +
        +
      • Demonstrating empathy and kindness toward other people
      • Being respectful of differing opinions, viewpoints, and experiences
      • Giving and gracefully accepting constructive feedback
      • Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
      • Focusing on what is best not just for us as individuals, but for the overall community
        • -

      Examples of unacceptable behavior include:

      -
      • The use of sexualized language or imagery, and sexual attention or advances of any kind
        • +
      +

      Examples of unacceptable behavior include:

      +
        +
      • The use of sexualized language or imagery, and sexual attention or advances of any kind
      • Trolling, insulting or derogatory comments, and personal or political attacks
      • Public or private harassment
      • Publishing others’ private information, such as a physical or email address, without their explicit permission
      • Other conduct which could reasonably be considered inappropriate in a professional setting
        • -
    + +
    -

    Enforcement Responsibilities

    +

    Enforcement Responsibilities +

    Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.

    Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.

    -

    Scope

    +

    Scope +

    This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.

    -

    Enforcement

    +

    Enforcement +

    Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at [INSERT CONTACT METHOD]. All complaints will be reviewed and investigated promptly and fairly.

    All community leaders are obligated to respect the privacy and security of the reporter of any incident.

    -

    Enforcement Guidelines

    +

    Enforcement Guidelines +

    Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:

    -

    1. Correction

    +

    1. Correction +

    Community Impact: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.

    Consequence: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.

    -

    2. Warning

    +

    2. Warning +

    Community Impact: A violation through a single incident or series of actions.

    Consequence: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.

    -

    3. Temporary Ban

    +

    3. Temporary Ban +

    Community Impact: A serious violation of community standards, including sustained inappropriate behavior.

    Consequence: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.

    -

    4. Permanent Ban

    +

    4. Permanent Ban +

    Community Impact: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.

    Consequence: A permanent ban from any sort of public interaction within the community.

    -

    Attribution

    +

    Attribution +

    This Code of Conduct is adapted from the Contributor Covenant, version 2.1, available at https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.

    Community Impact Guidelines were inspired by Mozilla’s code of conduct enforcement ladder.

    For answers to common questions about this code of conduct, see the FAQ at https://www.contributor-covenant.org/faq. Translations are available at https://www.contributor-covenant.org/translations.

    @@ -126,17 +161,19 @@

    Attribution

    + + + + - - + + diff --git a/v0.1.5/CONTRIBUTING.html b/v0.1.5/CONTRIBUTING.html index 5acd95aa..e4e98426 100644 --- a/v0.1.5/CONTRIBUTING.html +++ b/v0.1.5/CONTRIBUTING.html @@ -1,8 +1,22 @@ - -Contribution Guidelines • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -62,7 +82,8 @@

    🙏 Thank you for taking the time to contribute!

    Your input is deeply valued, whether an issue, a pull request, or even feedback, regardless of size, content or scope.

    -

    Table of contents

    +

    Table of contents +

    👶 Getting started

    📔 Code of Conduct

    🗃 License

    @@ -73,38 +94,47 @@

    Table of contents❓ Questions

    -

    Getting started

    +

    Getting started +

    Please refer the project documentation for a brief introduction. Please also see other articles within the project documentation for additional information.

    -

    Code of Conduct

    +

    Code of Conduct +

    A Code of Conduct governs this project. Participants and contributors are expected to follow the rules outlined therein.

    -

    License

    +

    License +

    All your contributions will be covered by this project’s license.

    -

    Issues

    +

    Issues +

    We use GitHub to track issues, feature requests, and bugs. Before submitting a new issue, please check if the issue has already been reported. If the issue already exists, please upvote the existing issue 👍.

    For new feature requests, please elaborate on the context and the benefit the feature will have for users, developers, or other relevant personas.

    -

    Pull requests

    +

    Pull requests +

    -

    GitHub Flow

    +

    GitHub Flow +

    This repository uses the GitHub Flow model for collaboration. To submit a pull request:

    -
    1. +
        +

      1. Create a branch

        Please see the branch naming convention below. If you don’t have write access to this repository, please fork it.

      2. Make changes

        Make sure your code

        -
        • passes all checks imposed by GitHub Actions
          • +
            +
          • passes all checks imposed by GitHub Actions
          • is well documented
          • is well tested with unit tests sufficiently covering the changes introduced
            • -
          +
        +

      3. Create a pull request (PR)

        In the pull request description, please link the relevant issue (if any), provide a detailed description of the change, and include any assumptions.

        @@ -118,76 +148,93 @@

        GitHub Flow -

        Branch naming convention

        +

        Branch naming convention +

        Suppose your changes are related to a current issue in the current project; please name your branch as follows: <issue_id>_<short_description>. Please use underscore (_) as a delimiter for word separation. For example, 420_fix_ui_bug would be a suitable branch name if your change is resolving and UI-related bug reported in issue number 420 in the current project.

        If your change affects multiple repositories, please name your branches as follows: <issue_id>_<issue_repo>_<short description>. For example, 69_awesomeproject_fix_spelling_error would reference issue 69 reported in project awesomeproject and aims to resolve one or more spelling errors in multiple (likely related) repositories.

    monorepo and staged.dependencies -

    + +

    Sometimes you might need to change upstream dependent package(s) to be able to submit a meaningful change. We are using staged.dependencies functionality to simulate a monorepo behavior. The dependency configuration is already specified in this project’s staged_dependencies.yaml file. You need to name the feature branches appropriately. This is the only exception from the branch naming convention described above.

    Please refer to the staged.dependencies package documentation for more details.

    -

    Coding guidelines

    +

    Coding guidelines +

    This repository follows some unified processes and standards adopted by its maintainers to ensure software development is carried out consistently within teams and cohesively across other repositories.

    -

    Style guide

    +

    Style guide +

    This repository follows the standard tidyverse style guide and uses lintr for lint checks. Customized lint configurations are available in this repository’s .lintr file.

    -

    Dependency management

    +

    Dependency management +

    Lightweight is the right weight. This repository follows tinyverse recommedations of limiting dependencies to minimum.

    -

    Dependency version management

    +

    Dependency version management +

    If the code is not compatible with all (!) historical versions of a given dependenct package, it is required to specify minimal version in the DESCRIPTION file. In particular: if the development version requires (imports) the development version of another package - it is required to put abc (>= 1.2.3.9000).

    -

    Recommended development environment & tools

    +

    Recommended development environment & tools +

    -

    R & package versions

    +

    R & package versions +

    We continuously test our packages against the newest R version along with the most recent dependencies from CRAN and BioConductor. We recommend that your working environment is also set up in the same way. You can find the details about the R version and packages used in the R CMD check GitHub Action execution log - there is a step that prints out the R sessionInfo().

    If you discover bugs on older R versions or with an older set of dependencies, please create the relevant bug reports.

    -

    pre-commit

    +

    +pre-commit +

    We highly recommend that you use the pre-commit tool combined with R hooks for pre-commit to execute some of the checks before committing and pushing your changes.

    Pre-commit hooks are already available in this repository’s .pre-commit-config.yaml file.

    -

    Recognition model

    +

    Recognition model +

    As mentioned previously, all contributions are deeply valued and appreciated. While all contribution data is available as part of the repository insights, to recognize a significant contribution and hence add the contributor to the package authors list, the following rules are enforced:

    -
    • Minimum 5% of lines of code authored* (determined by git blame query) OR
      • +
        +
      • Minimum 5% of lines of code authored* (determined by git blame query) OR
      • Being at the top 5 contributors in terms of number of commits OR lines added OR lines removed*
        • -

      *Excluding auto-generated code, including but not limited to roxygen comments or renv.lock files.

      +
    +

    *Excluding auto-generated code, including but not limited to roxygen comments or renv.lock files.

    The package maintainer also reserves the right to adjust the criteria to recognize contributions.

    -

    Questions

    +

    Questions +

    If you have further questions regarding the contribution guidelines, please contact the package/repository maintainer.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/LICENSE-text.html b/v0.1.5/LICENSE-text.html index b774669d..dc031e3d 100644 --- a/v0.1.5/LICENSE-text.html +++ b/v0.1.5/LICENSE-text.html @@ -1,8 +1,22 @@ - -License • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,17 +92,19 @@ limitations under the License. - + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/SECURITY.html b/v0.1.5/SECURITY.html index 9f8a6d8b..bf7db0b7 100644 --- a/v0.1.5/SECURITY.html +++ b/v0.1.5/SECURITY.html @@ -1,8 +1,22 @@ - -Security Policy • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -60,38 +80,44 @@
    -

    Reporting Security Issues

    +

    Reporting Security Issues +

    If you believe you have found a security vulnerability in any of the repositories in this organization, please report it to us through coordinated disclosure.

    Please do not report security vulnerabilities through public GitHub issues, discussions, or pull requests.

    Instead, please send an email to vulnerability.management[@]roche.com.

    Please include as much of the information listed below as you can to help us better understand and resolve the issue:

    -
    • The type of issue (e.g., buffer overflow, SQL injection, or cross-site scripting)
      • +
        +
      • The type of issue (e.g., buffer overflow, SQL injection, or cross-site scripting)
      • Full paths of source file(s) related to the manifestation of the issue
      • The location of the affected source code (tag/branch/commit or direct URL)
      • Any special configuration required to reproduce the issue
      • Step-by-step instructions to reproduce the issue
      • Proof-of-concept or exploit code (if possible)
      • Impact of the issue, including how an attacker might exploit the issue
        • -

      This information will help us triage your report more quickly.

      +
    +

    This information will help us triage your report more quickly.

    -

    Data Security Standards (DSS)

    +

    Data Security Standards (DSS) +

    Please make sure that while reporting issues in the form a bug, feature, or pull request, all sensitive information such as PII, PHI, and PCI is completely removed from any text and attachments, including pictures and videos.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/articles/Getting_Started.html b/v0.1.5/articles/Getting_Started.html index 32c6ede1..86b23eaf 100644 --- a/v0.1.5/articles/Getting_Started.html +++ b/v0.1.5/articles/Getting_Started.html @@ -1,5 +1,4 @@ - - + @@ -46,14 +45,15 @@ Changelog
  • -
    main + +
    + main latest-tag v0.1.6 v0.1.5 -v0.1.4
    • +v0.1.4 + + + + -
    • +
        +
        • -
      +
    + @@ -60,20 +80,25 @@

    All vignettes

    -
    Getting Started
    +
    +
    Getting Started
    -
    - + +
    + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/authors.html b/v0.1.5/authors.html index b90351c8..6e5951c1 100644 --- a/v0.1.5/authors.html +++ b/v0.1.5/authors.html @@ -1,8 +1,22 @@ - -Authors and Citation • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -59,7 +79,8 @@

    Authors

    -
    • +
        +

      • Daniel Sabanés Bové. Author, maintainer.

        • @@ -123,7 +144,8 @@

        Authors

        F. Hoffmann-La Roche AG. Copyright holder, funder.

        -
    + +

    Citation

    @@ -142,17 +164,19 @@

    Citation

    }
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/index.html b/v0.1.5/index.html index 33fd244d..5d089472 100644 --- a/v0.1.5/index.html +++ b/v0.1.5/index.html @@ -1,5 +1,4 @@ - - + @@ -46,14 +45,15 @@ Changelog
  • -
    main + +
    + main latest-tag v0.1.6 v0.1.5 -v0.1.4
    • +v0.1.4 + + + + -
    • +
        +
        • -
      +
    + @@ -58,65 +78,99 @@
    -

    teal.modules.hermes 0.1.5

    +

    teal.modules.hermes 0.1.5 +

    -

    Bug Fixes

    -
    • Filtering data with the filter panel now correctly triggers the sampleVarSpecModule.
      • -
    +

    Bug Fixes +

    +
      +
    • Filtering data with the filter panel now correctly triggers the sampleVarSpecModule.
      • +
    +
    -

    Breaking changes

    -
    • Replaced datasets argument containing FilteredData with the new arguments data (tdata object) and filter_panel_api (FilterPanelAPI).
      • -
    +

    Breaking changes +

    +
      +
    • Replaced datasets argument containing FilteredData with the new arguments data (tdata object) and filter_panel_api (FilterPanelAPI).
      • +
    +
    -

    Miscellaneous

    -
    • Removed scda from dependencies.
      • +

      Miscellaneous +

      +
        +
      • Removed scda from dependencies.
      • Migrate to shinytest2.
        • -
    + +
    -

    teal.modules.hermes 0.1.4

    -
    • Added the teal.reporter functionality to all modules.
      • +

      teal.modules.hermes 0.1.4 +

      +
        +
      • Added the teal.reporter functionality to all modules.
      • Add installation instruction
        • -
    + +
    -

    teal.modules.hermes 0.1.3

    -
    • Improve the selection of sample variables in the forest module (tm_g_forest_tte) such that only categorical variables can be selected in the first place.
      • -
    -

    Miscellaneous

    -
    • Added a template to the pkgdown site.
      • +

      teal.modules.hermes 0.1.3 +

      +
        +
      • Improve the selection of sample variables in the forest module (tm_g_forest_tte) such that only categorical variables can be selected in the first place.
        • +
      +
      +

      Miscellaneous +

      +
        +
      • Added a template to the pkgdown site.
      • Updated package authors.
      • Added the option categorical_only to the sampleVarSpec server module, which allows to only show categorical sample variables for selection.
        • -
      +
    +
    -

    teal.modules.hermes 0.1.2

    -
    • Rewrote modules to use moduleServer and updated call to plot_with_settings_srv after changes in teal.devel.
      • +

      teal.modules.hermes 0.1.2 +

      +
        +
      • Rewrote modules to use moduleServer and updated call to plot_with_settings_srv after changes in teal.devel.
      • Replaced calls to teal::root_modules with teal::modules following deprecation of teal::root_modules.
      • Added basic logging to the modules.
      • Fixed the geneSpecInput so that the hermes app doesn’t fail anymore (on chrome) on an experiment with no genes.
        • -
    + +
    -

    teal.modules.hermes 0.1.1

    +

    teal.modules.hermes 0.1.1 +

    -

    Bug Fixes

    -
    • Updated legend for the PCA plot.
      • +

      Bug Fixes +

      +
        +
      • Updated legend for the PCA plot.
      • Gene selection with more than a few thousand genes no longer hangs the application. This is achieved through a different selection input in the corresponding geneSpec shiny module.
      • Only atomic columns of colData with at least one value can now be selected in the sampleVarSpecModule.
        • -
    + +
    -

    Miscellaneous

    -
    • Updated R version requirement to >= 3.6.
      • +

      Miscellaneous +

      +
        +
      • Updated R version requirement to >= 3.6.
      • Updated sampleVarSpec and geneSpec modules with new icons to remove warnings when using shiny version >= 1.7.
      • Removed dependencies on deprecated packages utils.nest and test.nest.
        • -
    + +
    -

    teal.modules.hermes 0.1.0

    -
    • First release of the teal.modules.hermes package, which contains teal modules for RNA-seq analysis using the hermes package.
      • +

      teal.modules.hermes 0.1.0 +

      +
        +
      • First release of the teal.modules.hermes package, which contains teal modules for RNA-seq analysis using the hermes package.
      • New users should first begin by reading the README.md of the teal.modules.hermes package to become familiar.
        • -
      -

      New Features

      -
      • +
      +
      +

      New Features +

      +
      +
    +
    + + + + - - + + diff --git a/v0.1.5/pull_request_template.html b/v0.1.5/pull_request_template.html index 798bc355..2ef9490d 100644 --- a/v0.1.5/pull_request_template.html +++ b/v0.1.5/pull_request_template.html @@ -1,8 +1,22 @@ - -Pull Request • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,17 +83,19 @@

    Fixes #nnn

    - + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/reference/adtteSpecInput.html b/v0.1.5/reference/adtteSpecInput.html index c7b70974..04ce864c 100644 --- a/v0.1.5/reference/adtteSpecInput.html +++ b/v0.1.5/reference/adtteSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for ADTTE Specification — adtteSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,13 +88,16 @@
    -

    Usage

    +

    Usage +

    adtteSpecInput(inputId, label_paramcd = "Select Endpoint")
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -80,30 +105,35 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    adtteSpecServer() for the module server and a complete example.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/reference/adtteSpecServer.html b/v0.1.5/reference/adtteSpecServer.html index c912e28b..bdfa72a8 100644 --- a/v0.1.5/reference/adtteSpecServer.html +++ b/v0.1.5/reference/adtteSpecServer.html @@ -1,18 +1,34 @@ - - + + + + + +Module Server for ADTTE Specification — adtteSpecServer • teal.modules.hermes +Module Server for ADTTE Specification — adtteSpecServer • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -28,7 +44,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -78,7 +100,8 @@
    -

    Usage

    +

    Usage +

    adtteSpecServer(
   id,
   data,
@@ -94,8 +117,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -115,8 +140,11 @@

    ArgumentsArgumentsArguments -

    Value

    +

    Value +

    -

    List with the following elements:

    • binned_adtte_subset: reactive containing the joined ADTTE and gene data.

      • +

      List with the following elements:

      +
        +

      • binned_adtte_subset: reactive containing the joined ADTTE and gene data.

      • gene_col: reactive containing the string with the column name of the original numeric gene variable.

      • gene_factor: string with the variable name for the binned gene data.

      • time_unit: reactive string with the time unit for the current subset.

        • -
    + +
    -

    See also

    +

    See also +

    adtteSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                data) {
   ns <- NS(id)
@@ -259,17 +295,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/assaySpecInput.html b/v0.1.5/reference/assaySpecInput.html index 0a84d160..810c3e5b 100644 --- a/v0.1.5/reference/assaySpecInput.html +++ b/v0.1.5/reference/assaySpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Assay Specification — assaySpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,13 +88,16 @@
    -

    Usage

    +

    Usage +

    assaySpecInput(inputId, label_assays = "Select Assay")
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -80,30 +105,35 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    assaySpecServer() for the module server and a complete example.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/reference/assaySpecServer.html b/v0.1.5/reference/assaySpecServer.html index cacce77a..e3b2845f 100644 --- a/v0.1.5/reference/assaySpecServer.html +++ b/v0.1.5/reference/assaySpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Assay Specification — assaySpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,13 +88,16 @@
    -

    Usage

    +

    Usage +

    assaySpecServer(id, assays, exclude_assays = character())
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -84,20 +109,24 @@

    Arguments -

    Value

    +

    Value +

    The chosen assay as a reactive string.

    -

    See also

    +

    See also +

    assaySpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                data) {
   ns <- NS(id)
@@ -160,17 +189,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/assert_adtte_vars.html b/v0.1.5/reference/assert_adtte_vars.html index 5661d546..eb323647 100644 --- a/v0.1.5/reference/assert_adtte_vars.html +++ b/v0.1.5/reference/assert_adtte_vars.html @@ -1,10 +1,26 @@ - -Check for ADTTE Variables — assert_adtte_vars • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,38 +88,46 @@
    -

    Usage

    +

    Usage +

    assert_adtte_vars(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    -
    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    assert_adtte_vars(list(aval = "AV", is_event = "EV", paramcd = "PC", usubjid = "ID", avalu = "u"))
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/reference/assert_summary_funs.html b/v0.1.5/reference/assert_summary_funs.html index 1b37bfd6..49dbd257 100644 --- a/v0.1.5/reference/assert_summary_funs.html +++ b/v0.1.5/reference/assert_summary_funs.html @@ -1,10 +1,26 @@ - -Check for List of Summary Functions — assert_summary_funs • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,13 +88,16 @@
    -

    Usage

    +

    Usage +

    assert_summary_funs(x, null.ok = FALSE)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    @@ -80,29 +105,34 @@

    Arguments -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    assert_summary_funs(list(mean = colMeans, raw = NULL), null.ok = TRUE)
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/reference/assertion_arguments.html b/v0.1.5/reference/assertion_arguments.html index e378718b..7833dab1 100644 --- a/v0.1.5/reference/assertion_arguments.html +++ b/v0.1.5/reference/assertion_arguments.html @@ -1,10 +1,26 @@ - -Standard Assertion Arguments — assertion_arguments • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -67,8 +89,10 @@
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    @@ -95,19 +119,22 @@

    Argumentscheckmate::vname().

    -

    + + - + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/reference/assertions.html b/v0.1.5/reference/assertions.html index 6749d3b6..7ae9844b 100644 --- a/v0.1.5/reference/assertions.html +++ b/v0.1.5/reference/assertions.html @@ -1,14 +1,30 @@ - - + + + + + +Additional Assertions for checkmate — assertions • teal.modules.hermes +Additional Assertions for checkmate — assertions • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    +
    -

    Additional Assertions for checkmate

    +

    Additional Assertions for checkmate +

    Source: R/checkmate.R
    assertions.Rd
    @@ -73,32 +96,39 @@
    -

    Value

    +

    Value +

    -

    Depending on the function prefix.

    • assert_ functions return the object invisibly if successful, and otherwise +

      Depending on the function prefix.

      +
        +

      • assert_ functions return the object invisibly if successful, and otherwise throw an error message.

      • check_ functions return TRUE if successful, otherwise a string with the error message.

      • test_ functions just return TRUE or FALSE.

        • -
    + +
    -

    See also

    +

    See also +

    assert_tag(), assert_reactive(), assert_summary_funs(), assert_adtte_vars()

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/reference/check_reactive.html b/v0.1.5/reference/check_reactive.html index d59bc048..17599aae 100644 --- a/v0.1.5/reference/check_reactive.html +++ b/v0.1.5/reference/check_reactive.html @@ -1,10 +1,26 @@ - -Check for Reactive Input — check_reactive • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    check_reactive(x)
 
 assert_reactive(x, .var.name = checkmate::vname(x), add = NULL)
@@ -75,8 +98,10 @@ 
    Usage
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    @@ -89,14 +114,17 @@

    Argumentscheckmate::AssertCollection.

    -

    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    check_reactive("bla")
 #> [1] FALSE
 check_reactive(reactive("bla"))
@@ -104,17 +132,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/check_tag.html b/v0.1.5/reference/check_tag.html index ba4a2553..260df696 100644 --- a/v0.1.5/reference/check_tag.html +++ b/v0.1.5/reference/check_tag.html @@ -1,10 +1,26 @@ - -Check for Shiny Tag — check_tag • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    check_tag(x, null.ok = FALSE)
 
 assert_tag(x, null.ok = FALSE, .var.name = checkmate::vname(x), add = NULL)
@@ -77,8 +100,10 @@ 
    Usage
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    @@ -105,14 +130,17 @@

    Argumentscheckmate::vname().

    -

    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    check_tag("bla")
 #> [1] "Must be a 'shiny.tag' or NULL"
 check_tag(NULL, null.ok = TRUE)
@@ -120,17 +148,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/experimentSpecInput.html b/v0.1.5/reference/experimentSpecInput.html index 6b04d9fa..06492158 100644 --- a/v0.1.5/reference/experimentSpecInput.html +++ b/v0.1.5/reference/experimentSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Experiment Specification — experimentSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    experimentSpecInput(
   inputId,
   data,
@@ -76,8 +99,10 @@ 
    Usage
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -95,30 +120,35 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    experimentSpecServer() for the module server and a complete example.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/reference/experimentSpecServer.html b/v0.1.5/reference/experimentSpecServer.html index b688de85..878a68a9 100644 --- a/v0.1.5/reference/experimentSpecServer.html +++ b/v0.1.5/reference/experimentSpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Experiment Specification — experimentSpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    experimentSpecServer(
   id,
   data,
@@ -79,8 +102,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -113,23 +138,30 @@

    Arguments -

    Value

    +

    Value +

    -

    List with the following reactive objects:

    • data: the hermes::AnyHermesData experiment.

      • +

      List with the following reactive objects:

      +
        +

      • data: the hermes::AnyHermesData experiment.

      • name: the name of the experiment as selected by the user.

      • genes: a data.frame with the genes in data, with columns id and name.

      • assays: the names of the assays in data.

        • -
    + +
    -

    See also

    +

    See also +

    experimentSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                data,
                mae_name) {
@@ -211,17 +243,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/function_arguments.html b/v0.1.5/reference/function_arguments.html index bb77d972..e08de9bc 100644 --- a/v0.1.5/reference/function_arguments.html +++ b/v0.1.5/reference/function_arguments.html @@ -1,10 +1,26 @@ - -Standard Function Arguments — function_arguments • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -67,8 +89,10 @@
    -

    Arguments

    -
    adtte
    +

    Arguments +

    +
    +
    adtte

    (data frame)
    an adtte dataset.

    @@ -96,19 +120,22 @@

    Arguments

    teal.modules.hermes is a part of the NEST and pharmaverse.

    - + + - - + + diff --git a/v0.1.5/reference/geneSpecInput.html b/v0.1.5/reference/geneSpecInput.html index bd03d487..2a2818b5 100644 --- a/v0.1.5/reference/geneSpecInput.html +++ b/v0.1.5/reference/geneSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Gene Signature Specification — geneSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    geneSpecInput(
   inputId,
   funs,
@@ -83,8 +106,10 @@ 
    Usage
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -126,20 +151,24 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    geneSpecServer() for the module server and a complete example.

    -

    Examples

    +

    Examples +

    geneSpecInput("my_genes", list(mean = colMeans), label_funs = "Please select function")
 #> <div class="row">
 #>   <div class="col-sm-8">
@@ -205,17 +234,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/geneSpecServer.html b/v0.1.5/reference/geneSpecServer.html index a6192702..66d00e74 100644 --- a/v0.1.5/reference/geneSpecServer.html +++ b/v0.1.5/reference/geneSpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Gene Signature Specification — geneSpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    geneSpecServer(
   id,
   funs,
@@ -78,8 +101,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -100,21 +125,25 @@

    Arguments -

    Value

    +

    Value +

    Reactive hermes::GeneSpec which can be used as input for the relevant hermes functions.

    -

    See also

    +

    See also +

    geneSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                data,
                funs) {
@@ -186,17 +215,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/h_assign_to_group_list.html b/v0.1.5/reference/h_assign_to_group_list.html index 29924f0d..3f64277d 100644 --- a/v0.1.5/reference/h_assign_to_group_list.html +++ b/v0.1.5/reference/h_assign_to_group_list.html @@ -1,12 +1,28 @@ - - + + + + + +Helper Function For Group List Creation — h_assign_to_group_list • teal.modules.hermes +Helper Function For Group List Creation — h_assign_to_group_list • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,25 +91,31 @@
    -

    Usage

    +

    Usage +

    h_assign_to_group_list(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (named list of character)
    input assignment list.

    -
    + +
    -

    Value

    +

    Value +

    A combination list.

    -

    Examples

    +

    Examples +

    assign_list <- list(
   "ASIAN" = "1",
   "BLACK OR AFRICAN AMERICAN" = "1",
@@ -105,17 +133,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/h_collapse_levels.html b/v0.1.5/reference/h_collapse_levels.html index b825e309..5d697c90 100644 --- a/v0.1.5/reference/h_collapse_levels.html +++ b/v0.1.5/reference/h_collapse_levels.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function for Collapsing of Factor Levels — h_collapse_levels • teal.modules.hermes +Helper Function for Collapsing of Factor Levels — h_collapse_levels • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,13 +94,16 @@
    -

    Usage

    +

    Usage +

    h_collapse_levels(x, group_list)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (factor)
    original factor.

    @@ -86,16 +111,19 @@

    Arguments -

    Value

    +

    Value +

    The transformed factor x with new levels.

    -

    Examples

    +

    Examples +

    set.seed(123)
 x <- factor(sample(
   c("ASIAN", "BLACK OR AFRICAN AMERICAN", "MULTIPLE", "UNKNOWN", "WHITE"),
@@ -112,17 +140,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/h_extract_words.html b/v0.1.5/reference/h_extract_words.html index 04fe36b8..ca3387c8 100644 --- a/v0.1.5/reference/h_extract_words.html +++ b/v0.1.5/reference/h_extract_words.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Extract Words — h_extract_words • teal.modules.hermes +Helper Function to Extract Words — h_extract_words • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,25 +94,31 @@
    -

    Usage

    +

    Usage +

    h_extract_words(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (string)
    input.

    -
    + +
    -

    Value

    +

    Value +

    Character vector with the extracted words.

    -

    Examples

    +

    Examples +

    h_extract_words("a, b, , c, 234; 34562 - GeneID:bla")
 #> [1] "a"          "b"          "c"          "234"        "34562"     
 #> [6] "GeneID:bla"
@@ -99,17 +127,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/h_gene_data.html b/v0.1.5/reference/h_gene_data.html index ea91af19..4ad56671 100644 --- a/v0.1.5/reference/h_gene_data.html +++ b/v0.1.5/reference/h_gene_data.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Format Gene Choices — h_gene_data • teal.modules.hermes +Helper Function to Format Gene Choices — h_gene_data • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,13 +94,16 @@
    -

    Usage

    +

    Usage +

    h_gene_data(object, name_annotation)
    -

    Arguments

    -
    object
    +

    Arguments +

    +
    +
    object

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    @@ -87,23 +112,27 @@

    Arguments -

    Value

    +

    Value +

    A data.frame with id and name columns containing all genes from object.

    -

    Details

    +

    Details +

    Note that missing names or names that only contain whitespace are replaced by empty strings for consistency and better labeling in the UI downstream

    -

    Examples

    +

    Examples +

    object <- hermes::hermes_data[1:10, ]
 h_gene_data(object, "symbol")
 #>                  id         name
@@ -120,17 +149,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/h_km_mae_to_adtte.html b/v0.1.5/reference/h_km_mae_to_adtte.html index 48d176c9..a0ec01db 100644 --- a/v0.1.5/reference/h_km_mae_to_adtte.html +++ b/v0.1.5/reference/h_km_mae_to_adtte.html @@ -1,10 +1,26 @@ - -Data Preprocessing for ADTTE Module — h_km_mae_to_adtte • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    h_km_mae_to_adtte(
   adtte,
   mae,
@@ -78,8 +101,10 @@ 
    Usage
    -

    Arguments

    -
    adtte
    +

    Arguments +

    +
    +
    adtte

    (data frame)
    an adtte dataset.

    @@ -103,9 +128,11 @@

    Arguments -

    Value

    +

    Value +

    A data frame containing all columns/rows from adtte that match @@ -114,13 +141,15 @@

    Value

    -

    Note

    +

    Note +

    The final gene column names can start with a different string than the original gene IDs (or labels), in particular white space and colons are removed.

    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 adtte <- teal.modules.hermes::rADTTE %>%
   dplyr::mutate(CNSR = as.logical(CNSR))
@@ -146,17 +175,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/h_order_genes.html b/v0.1.5/reference/h_order_genes.html index f55fd573..ae7c68ca 100644 --- a/v0.1.5/reference/h_order_genes.html +++ b/v0.1.5/reference/h_order_genes.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Order Gene Choices — h_order_genes • teal.modules.hermes +Helper Function to Order Gene Choices — h_order_genes • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,26 +94,32 @@
    -

    Usage

    +

    Usage +

    h_order_genes(genes)
    -

    Arguments

    -
    genes
    +

    Arguments +

    +
    +
    genes

    (data.frame)
    containing id and name columns of the gene choices. Note that no missing values are allowed.

    -
    + +
    -

    Value

    +

    Value +

    The ordered data.frame.

    -

    Examples

    +

    Examples +

    genes <- data.frame(
   id = c("7", "1", "2", "345346", "0"),
   name = c("e", "", "c", "", "a")
@@ -106,17 +134,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/h_parse_genes.html b/v0.1.5/reference/h_parse_genes.html index 690a0590..19ed1700 100644 --- a/v0.1.5/reference/h_parse_genes.html +++ b/v0.1.5/reference/h_parse_genes.html @@ -1,12 +1,28 @@ - - + + + + + +Helper Function to Parse Genes — h_parse_genes • teal.modules.hermes +Helper Function to Parse Genes — h_parse_genes • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,13 +91,16 @@
    -

    Usage

    +

    Usage +

    h_parse_genes(words, choices)
    -

    Arguments

    -
    words
    +

    Arguments +

    +
    +
    words

    (character)
    containing gene IDs or names.

    @@ -83,16 +108,19 @@

    Arguments -

    Value

    +

    Value +

    The subset of choices which matches words in ID or name.

    -

    Examples

    +

    Examples +

    h_parse_genes(
   c("a", "2535"),
   data.frame(id = as.character(2533:2537), name = letters[1:5])
@@ -103,17 +131,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/h_update_gene_selection.html b/v0.1.5/reference/h_update_gene_selection.html index f8f02642..178a9a26 100644 --- a/v0.1.5/reference/h_update_gene_selection.html +++ b/v0.1.5/reference/h_update_gene_selection.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Update Gene Selection — h_update_gene_selection • teal.modules.hermes +Helper Function to Update Gene Selection — h_update_gene_selection • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,13 +94,16 @@
    -

    Usage

    +

    Usage +

    h_update_gene_selection(session, inputId, selected, choices)
    -

    Arguments

    -
    session
    +

    Arguments +

    +
    +
    session

    (ShinySession)
    the session object.

    @@ -95,20 +120,23 @@

    Arguments

    + + + + - - + + diff --git a/v0.1.5/reference/heatmap_plot.html b/v0.1.5/reference/heatmap_plot.html index 3068ed46..38f1a8d1 100644 --- a/v0.1.5/reference/heatmap_plot.html +++ b/v0.1.5/reference/heatmap_plot.html @@ -1,10 +1,26 @@ - -Correlation Heatmap Plot — heatmap_plot • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,29 +88,35 @@
    -

    Usage

    +

    Usage +

    heatmap_plot(object, assay_name)
    -

    Arguments

    -
    object
    +

    Arguments +

    +
    +
    object

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    assay_name

    (string)
    the assay to define the groups.

    -
    + +
    -

    Value

    +

    Value +

    Plot to be displayed in the teal app.

    -

    Examples

    +

    Examples +

    library(hermes)
 #> Loading required package: ggfortify
 #> Loading required package: SummarizedExperiment
@@ -169,17 +197,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/include_css_files.html b/v0.1.5/reference/include_css_files.html index 0712f80e..1486f639 100644 --- a/v0.1.5/reference/include_css_files.html +++ b/v0.1.5/reference/include_css_files.html @@ -1,12 +1,28 @@ - - + + + + + +Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.modules.hermes +Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,35 +91,42 @@
    -

    Usage

    +

    Usage +

    include_css_files(pattern = "*")
    -

    Arguments

    -
    pattern
    +

    Arguments +

    +
    +
    pattern

    (character) pattern of files to be included

    -
    + +
    -

    Value

    +

    Value +

    HTML code that includes CSS files

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/reference/include_js_files.html b/v0.1.5/reference/include_js_files.html index 97aa2137..b77aa511 100644 --- a/v0.1.5/reference/include_js_files.html +++ b/v0.1.5/reference/include_js_files.html @@ -1,12 +1,28 @@ - - + + + + + +Include JS files from /inst/js/ package directory to application header — include_js_files • teal.modules.hermes +Include JS files from /inst/js/ package directory to application header — include_js_files • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,39 +91,46 @@
    -

    Usage

    +

    Usage +

    include_js_files(pattern = "*")
    -

    Arguments

    -
    pattern
    +

    Arguments +

    +
    +
    pattern

    (character) pattern of files to be included, passed to system.file

    except

    (character) vector of basename filenames to be excluded

    -
    + +
    -

    Value

    +

    Value +

    HTML code that includes JS files

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/reference/index.html b/v0.1.5/reference/index.html index 00d20de2..a1f26b55 100644 --- a/v0.1.5/reference/index.html +++ b/v0.1.5/reference/index.html @@ -1,8 +1,22 @@ - -Function reference • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -57,280 +77,377 @@
    -

    Package

    +

    Package +

    -
    +
    +
    -
    +
    +
    teal.modules.hermes teal.modules.hermes-package
    -
    teal.modules.hermes Package
    -
    -

    Utility Functions

    +
    +teal.modules.hermes Package
    + +
    +
    +

    Utility Functions +

    -
    +
    +
    -
    +
    +
    h_assign_to_group_list()
    Helper Function For Group List Creation
    -
    +
    +
    +
    h_collapse_levels()
    Helper Function for Collapsing of Factor Levels
    -
    +
    +
    +
    h_extract_words()
    Helper Function to Extract Words
    -
    +
    +
    +
    h_gene_data()
    Helper Function to Format Gene Choices
    -
    +
    +
    +
    h_km_mae_to_adtte()
    Data Preprocessing for ADTTE Module
    -
    +
    +
    +
    h_order_genes()
    Helper Function to Order Gene Choices
    -
    +
    +
    +
    h_parse_genes()
    Helper Function to Parse Genes
    -
    +
    +
    +
    h_update_gene_selection()
    Helper Function to Update Gene Selection
    -
    +
    +
    +
    is_blank()
    Checking for Empty String
    -
    -

    Shiny Modules

    + +
    +
    +

    Shiny Modules +

    -
    +
    +
    -
    +
    +
    adtteSpecInput()
    Module Input for ADTTE Specification
    -
    +
    +
    +
    adtteSpecServer()
    Module Server for ADTTE Specification
    -
    +
    +
    +
    assaySpecInput()
    Module Input for Assay Specification
    -
    +
    +
    +
    assaySpecServer()
    Module Server for Assay Specification
    -
    +
    +
    +
    experimentSpecInput()
    Module Input for Experiment Specification
    -
    +
    +
    +
    experimentSpecServer()
    Module Server for Experiment Specification
    -
    +
    +
    +
    geneSpecInput()
    Module Input for Gene Signature Specification
    -
    +
    +
    +
    geneSpecServer()
    Module Server for Gene Signature Specification
    -
    +
    +
    +
    sampleVarSpecInput()
    Module Input for Sample Variable Specification
    -
    +
    +
    +
    sampleVarSpecServer()
    Module Server for Sample Variable Specification
    -
    +
    +
    +
    multiSampleVarSpecServer()
    Module Server for Specification of Multiple Sample Variables
    -
    -

    Teal Module Functions

    + +
    +
    +

    Teal Module Functions +

    -
    +
    +
    -
    +
    +
    tm_g_barplot() ui_g_barplot() srv_g_barplot() sample_tm_g_barplot()
    Teal Module for RNA-seq Barplot
    -
    +
    +
    +
    tm_g_boxplot() ui_g_boxplot() srv_g_boxplot() sample_tm_g_boxplot()
    Teal Module for RNA-seq Boxplot
    -
    +
    +
    +
    tm_g_forest_tte() ui_g_forest_tte() srv_g_forest_tte() sample_tm_g_forest_tte()
    Teal Module for Survival Forest Plot
    -
    +
    +
    +
    tm_g_km() ui_g_km() srv_g_km() sample_tm_g_km()
    Teal Module for Kaplan-Meier Plot
    -
    +
    +
    +
    tm_g_pca() ui_g_pca() srv_g_pca() sample_tm_g_pca()
    Teal Module for PCA Analysis
    -
    +
    +
    +
    tm_g_quality() ui_g_quality() srv_g_quality() sample_tm_g_quality()
    Teal Module for RNA-seq Quality Control
    -
    +
    +
    +
    tm_g_scatterplot() ui_g_scatterplot() srv_g_scatterplot() sample_tm_g_scatterplot()
    Teal Module for RNA-seq Scatterplot
    -
    +
    +
    +
    tm_g_volcanoplot() ui_g_volcanoplot() srv_g_volcanoplot() sample_tm_g_volcanoplot()
    Teal Module for RNA-seq Volcano Plot
    -
    -

    Graph Functions

    + +
    +
    +

    Graph Functions +

    -
    +
    +
    -
    +
    +
    heatmap_plot()
    Correlation Heatmap Plot
    -
    +
    +
    +
    top_gene_plot()
    Most Expressed Genes Plot
    -
    -

    Assertions

    + +
    +
    +

    Assertions +

    -
    +
    +
    -
    +
    +
    assert_adtte_vars()
    Check for ADTTE Variables
    -
    +
    +
    +
    check_reactive() assert_reactive() test_reactive()
    Check for Reactive Input
    -
    +
    +
    +
    assert_summary_funs()
    Check for List of Summary Functions
    -
    +
    +
    +
    check_tag() assert_tag() test_tag() expect_tag()
    Check for Shiny Tag
    -
    -

    Validations

    + +
    +
    +

    Validations +

    -
    +
    +
    -
    +
    +
    validate_gene_spec()
    Validation of Gene Specification
    -
    +
    +
    +
    validate_n_levels()
    Validation of Number of Levels
    -
    + + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/reference/is_blank.html b/v0.1.5/reference/is_blank.html index 78d0c333..c8236a30 100644 --- a/v0.1.5/reference/is_blank.html +++ b/v0.1.5/reference/is_blank.html @@ -1,12 +1,28 @@ - - + + + + + +Checking for Empty String — is_blank • teal.modules.hermes +Checking for Empty String — is_blank • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,25 +91,31 @@
    -

    Usage

    +

    Usage +

    is_blank(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    object to check.

    -
    + +
    -

    Value

    +

    Value +

    Flag whether x is identical to an empty string, i.e. "".

    -

    Examples

    +

    Examples +

    is_blank("")
 #> [1] TRUE
 is_blank(" ")
@@ -95,17 +123,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/module_arguments.html b/v0.1.5/reference/module_arguments.html index 1b9d551c..e953574a 100644 --- a/v0.1.5/reference/module_arguments.html +++ b/v0.1.5/reference/module_arguments.html @@ -1,10 +1,26 @@ - -Standard Module Arguments — module_arguments • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -67,8 +89,10 @@
    -

    Arguments

    -
    data
    +

    Arguments +

    +
    +
    data

    (tdata)
    tdata object which is automatically passed to the UI and server functions, holding all the data sets provided in the app initialization.

    @@ -89,8 +113,11 @@

    ArgumentsArgumentsArguments

    teal.modules.hermes is a part of the NEST and pharmaverse.

    - + + - - + + diff --git a/v0.1.5/reference/multiSampleVarSpecServer.html b/v0.1.5/reference/multiSampleVarSpecServer.html index acf6819f..c4a2ffc3 100644 --- a/v0.1.5/reference/multiSampleVarSpecServer.html +++ b/v0.1.5/reference/multiSampleVarSpecServer.html @@ -1,12 +1,28 @@ - - + + + + + +Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer • teal.modules.hermes +Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,13 +91,16 @@
    -

    Usage

    +

    Usage +

    multiSampleVarSpecServer(inputIds, original_data, ...)
    -

    Arguments

    -
    inputIds
    +

    Arguments +

    +
    +
    inputIds

    (character)
    multiple input IDs corresponding to the different sample variables specified in the UI function.

    @@ -93,9 +118,11 @@

    Arguments -

    Value

    +

    Value +

    List with the final transformed experiment_data reactive and a @@ -104,7 +131,8 @@

    Value

    -

    Examples

    +

    Examples +

    if (FALSE) {
 # In the server use:
 sample_var_specs <- multiSampleVarSpecServer(
@@ -122,17 +150,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/rADTTE.html b/v0.1.5/reference/rADTTE.html index 9b9af598..281d030d 100644 --- a/v0.1.5/reference/rADTTE.html +++ b/v0.1.5/reference/rADTTE.html @@ -1,8 +1,24 @@ - -Random Time to Event Analysis Dataset — rADTTE • teal.modules.hermes + + + + + + + + Skip to contents @@ -18,7 +34,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,31 +85,36 @@
    -

    Usage

    +

    Usage +

    rADTTE
    -

    Format

    +

    Format +

    An object of class tbl_df (inherits from tbl, data.frame) with 2000 rows and 67 columns.

    -

    Source

    +

    Source +

    internal

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/reference/sampleVarSpecInput.html b/v0.1.5/reference/sampleVarSpecInput.html index d53114f6..bea3eaa0 100644 --- a/v0.1.5/reference/sampleVarSpecInput.html +++ b/v0.1.5/reference/sampleVarSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Sample Variable Specification — sampleVarSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    sampleVarSpecInput(
   inputId,
   label_vars = "Select sample variable",
@@ -75,8 +98,10 @@ 
    Usage
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -88,20 +113,24 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    sampleVarSpecServer() for the module server and a complete example.

    -

    Examples

    +

    Examples +

    sampleVarSpecInput("my_vars", label_vars = "Select faceting variable")
 #> <div class="row">
 #>   <div class="col-sm-8">
@@ -124,17 +153,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/sampleVarSpecServer.html b/v0.1.5/reference/sampleVarSpecServer.html index ebe09b4b..fb011ce7 100644 --- a/v0.1.5/reference/sampleVarSpecServer.html +++ b/v0.1.5/reference/sampleVarSpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Sample Variable Specification — sampleVarSpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    sampleVarSpecServer(
   id,
   experiment_name,
@@ -81,8 +104,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -125,27 +150,32 @@

    Arguments -

    Value

    +

    Value +

    Reactive SummarizedExperiment::SummarizedExperiment which can be used as input for the relevant hermes functions.

    -

    Note

    +

    Note +

    Only atomic columns (e.g. not DataFrame columns) of the colData which are not completely missing (NA) will be shown for selection. If num_levels is specified then only factor columns will be available.

    -

    See also

    +

    See also +

    sampleVarSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                data) {
   ns <- NS(id)
@@ -212,17 +242,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/teal.modules.hermes-package.html b/v0.1.5/reference/teal.modules.hermes-package.html index 2be505b6..943f4d73 100644 --- a/v0.1.5/reference/teal.modules.hermes-package.html +++ b/v0.1.5/reference/teal.modules.hermes-package.html @@ -1,10 +1,26 @@ - -teal.modules.hermes Package — teal.modules.hermes-package • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    +
    -

    teal.modules.hermes Package

    +

    +teal.modules.hermes Package

    Source: R/package.R
    teal.modules.hermes-package.Rd
    @@ -67,15 +90,23 @@
    -

    See also

    -

    Useful links:

    +
    -

    Author

    +

    Author +

    Maintainer: Daniel Sabanés Bové daniel.sabanes_bove@roche.com

    -

    Authors:

    • Nikolas Burkoff

      • +

      Authors:

      +
        +

      • Nikolas Burkoff

      • Dinakar Kulkarni

      • Konrad Pagacz

      • Namrata Bhatia

        • @@ -85,25 +116,31 @@

        Author<

      • Stefanie Bienert

      • Haocheng Li

      • Lyndsee Midori Zhang

        • -

      Other contributors:

      • Sorin Voicu [contributor]

        • +
      +

      Other contributors:

      +
        +

      • Sorin Voicu [contributor]

      • Benoit Falquet [contributor]

      • Mahmoud Hallal [contributor]

      • Tim Treis [contributor]

      • F. Hoffmann-La Roche AG [copyright holder, funder]

        • -
    + +
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/reference/tm_g_barplot.html b/v0.1.5/reference/tm_g_barplot.html index 6bb75790..31963ac6 100644 --- a/v0.1.5/reference/tm_g_barplot.html +++ b/v0.1.5/reference/tm_g_barplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Barplot — tm_g_barplot • teal.modules.hermes +Teal Module for RNA-seq Barplot — tm_g_barplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_barplot(
   label,
   mae_name,
@@ -96,8 +119,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -145,23 +170,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_barplot(): sets up the user interface.

      • +
        +

      • ui_g_barplot(): sets up the user interface.

      • srv_g_barplot(): sets up the server with reactive graph.

      • sample_tm_g_barplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -186,17 +217,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/tm_g_boxplot.html b/v0.1.5/reference/tm_g_boxplot.html index 29f43177..43b86180 100644 --- a/v0.1.5/reference/tm_g_boxplot.html +++ b/v0.1.5/reference/tm_g_boxplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Boxplot — tm_g_boxplot • teal.modules.hermes +Teal Module for RNA-seq Boxplot — tm_g_boxplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_boxplot(
   label,
   mae_name,
@@ -96,8 +119,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -145,23 +170,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_boxplot(): sets up the user interface.

      • +
        +

      • ui_g_boxplot(): sets up the user interface.

      • srv_g_boxplot(): sets up the server with reactive graph.

      • sample_tm_g_boxplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -186,17 +217,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/tm_g_forest_tte.html b/v0.1.5/reference/tm_g_forest_tte.html index 239fd88c..227a3dfc 100644 --- a/v0.1.5/reference/tm_g_forest_tte.html +++ b/v0.1.5/reference/tm_g_forest_tte.html @@ -1,10 +1,26 @@ - -Teal Module for Survival Forest Plot — tm_g_forest_tte • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    tm_g_forest_tte(
   label,
   adtte_name,
@@ -110,8 +133,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -127,8 +152,11 @@

    ArgumentsArgumentsArguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_forest_tte(): sets up the user interface.

      • +
        +

      • ui_g_forest_tte(): sets up the user interface.

      • srv_g_forest_tte(): sets up the server with reactive graph.

      • sample_tm_g_forest_tte(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 adtte <- teal.modules.hermes::rADTTE %>%
   dplyr::mutate(is_event = (.data$CNSR == 0))
@@ -239,17 +274,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/tm_g_km.html b/v0.1.5/reference/tm_g_km.html index 3be82679..7f9124be 100644 --- a/v0.1.5/reference/tm_g_km.html +++ b/v0.1.5/reference/tm_g_km.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for Kaplan-Meier Plot — tm_g_km • teal.modules.hermes +Teal Module for Kaplan-Meier Plot — tm_g_km • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_km(
   label,
   adtte_name,
@@ -101,8 +124,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -118,8 +143,11 @@

    ArgumentsArgumentsArguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_km(): sets up the user interface.

      • +
        +

      • ui_g_km(): sets up the user interface.

      • srv_g_km(): sets up the user interface.

      • sample_tm_g_km(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 adtte <- teal.modules.hermes::rADTTE %>%
   dplyr::mutate(is_event = (.data$CNSR == 0))
@@ -224,17 +259,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/tm_g_pca.html b/v0.1.5/reference/tm_g_pca.html index 0ce4b7c5..2e5875ec 100644 --- a/v0.1.5/reference/tm_g_pca.html +++ b/v0.1.5/reference/tm_g_pca.html @@ -1,14 +1,30 @@ - - + + + + + +Teal Module for PCA Analysis — tm_g_pca • teal.modules.hermes +Teal Module for PCA Analysis — tm_g_pca • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,7 +94,8 @@
    -

    Usage

    +

    Usage +

    tm_g_pca(
   label,
   mae_name,
@@ -89,8 +112,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -132,23 +157,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_pca(): sets up the user interface.

      • +
        +

      • ui_g_pca(): sets up the user interface.

      • srv_g_pca(): sets up the server with reactive graph.

      • sample_tm_g_pca(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -173,17 +204,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/tm_g_quality.html b/v0.1.5/reference/tm_g_quality.html index 59805cd8..5db3a18f 100644 --- a/v0.1.5/reference/tm_g_quality.html +++ b/v0.1.5/reference/tm_g_quality.html @@ -1,14 +1,30 @@ - - + + + + + +Teal Module for RNA-seq Quality Control — tm_g_quality • teal.modules.hermes +Teal Module for RNA-seq Quality Control — tm_g_quality • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,7 +94,8 @@
    -

    Usage

    +

    Usage +

    tm_g_quality(
   label,
   mae_name,
@@ -89,8 +112,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -132,23 +157,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_quality(): sets up the user interface.

      • +
        +

      • ui_g_quality(): sets up the user interface.

      • srv_g_quality(): sets up the server with reactive graphs.

      • sample_tm_g_quality(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -172,17 +203,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/tm_g_scatterplot.html b/v0.1.5/reference/tm_g_scatterplot.html index 7cec6bb4..08ad5b7d 100644 --- a/v0.1.5/reference/tm_g_scatterplot.html +++ b/v0.1.5/reference/tm_g_scatterplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Scatterplot — tm_g_scatterplot • teal.modules.hermes +Teal Module for RNA-seq Scatterplot — tm_g_scatterplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_scatterplot(
   label,
   mae_name,
@@ -96,8 +119,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -145,23 +170,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_scatterplot(): sets up the user interface.

      • +
        +

      • ui_g_scatterplot(): sets up the user interface.

      • srv_g_scatterplot(): sets up the server with reactive graph.

      • sample_tm_g_scatterplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -186,17 +217,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/tm_g_volcanoplot.html b/v0.1.5/reference/tm_g_volcanoplot.html index 21b94ed8..07624649 100644 --- a/v0.1.5/reference/tm_g_volcanoplot.html +++ b/v0.1.5/reference/tm_g_volcanoplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot • teal.modules.hermes +Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_volcanoplot(
   label,
   mae_name,
@@ -93,8 +116,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -136,23 +161,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_volcanoplot(): sets up the user interface.

      • +
        +

      • ui_g_volcanoplot(): sets up the user interface.

      • srv_g_volcanoplot(): sets up the server with reactive graph.

      • sample_tm_g_volcanoplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 mae_data <- dataset("MAE", mae)
 data <- teal_data(mae_data)
@@ -177,17 +208,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.5/reference/top_gene_plot.html b/v0.1.5/reference/top_gene_plot.html index a5d207e2..3cd1037b 100644 --- a/v0.1.5/reference/top_gene_plot.html +++ b/v0.1.5/reference/top_gene_plot.html @@ -1,10 +1,26 @@ - -Most Expressed Genes Plot — top_gene_plot • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,46 +88,54 @@
    -

    Usage

    +

    Usage +

    top_gene_plot(object, assay_name)
    -

    Arguments

    -
    object
    +

    Arguments +

    +
    +
    object

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    assay_name

    (string)
    the assay to define the groups.

    -
    + +
    -

    Value

    +

    Value +

    Plot to be displayed in the teal app.

    -

    Examples

    +

    Examples +

    library(hermes)
 object <- HermesData(summarized_experiment)
 result <- top_gene_plot(object, assay_name = "counts")
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/reference/validate_gene_spec.html b/v0.1.5/reference/validate_gene_spec.html index 0522dc65..29c67e29 100644 --- a/v0.1.5/reference/validate_gene_spec.html +++ b/v0.1.5/reference/validate_gene_spec.html @@ -1,12 +1,28 @@ - - + + + + + +Validation of Gene Specification — validate_gene_spec • teal.modules.hermes +Validation of Gene Specification — validate_gene_spec • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,33 +91,39 @@
    -

    Usage

    +

    Usage +

    validate_gene_spec(gene_spec, gene_choices)
    -

    Arguments

    -
    gene_spec
    +

    Arguments +

    +
    +
    gene_spec

    (GeneSpec)
    gene specification.

    gene_choices

    (character)
    all possible gene choices.

    -
    + + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.5/reference/validate_n_levels.html b/v0.1.5/reference/validate_n_levels.html index f5d2c705..aa072a8a 100644 --- a/v0.1.5/reference/validate_n_levels.html +++ b/v0.1.5/reference/validate_n_levels.html @@ -1,12 +1,28 @@ - - + + + + + +Validation of Number of Levels — validate_n_levels • teal.modules.hermes +Validation of Number of Levels — validate_n_levels • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,13 +91,16 @@
    -

    Usage

    +

    Usage +

    validate_n_levels(x, name, n_levels)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (factor)
    factor to validate.

    @@ -86,20 +111,23 @@

    Arguments

    + + + + - - + + diff --git a/v0.1.6/404.html b/v0.1.6/404.html index 121d7de9..69162f4e 100644 --- a/v0.1.6/404.html +++ b/v0.1.6/404.html @@ -1,5 +1,4 @@ - - + @@ -44,14 +43,15 @@ Changelog
  • -
    main + +
    + main latest-tag v0.1.6 v0.1.5 -v0.1.4
    • +v0.1.4 + + + + -
    • +
        +
        • -
      +
    + @@ -60,65 +80,80 @@
    -

    Our Pledge

    +

    Our Pledge +

    We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.

    We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.

    -

    Our Standards

    +

    Our Standards +

    Examples of behavior that contributes to a positive environment for our community include:

    -
    • Demonstrating empathy and kindness toward other people
      • +
        +
      • Demonstrating empathy and kindness toward other people
      • Being respectful of differing opinions, viewpoints, and experiences
      • Giving and gracefully accepting constructive feedback
      • Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
      • Focusing on what is best not just for us as individuals, but for the overall community
        • -

      Examples of unacceptable behavior include:

      -
      • The use of sexualized language or imagery, and sexual attention or advances of any kind
        • +
      +

      Examples of unacceptable behavior include:

      +
        +
      • The use of sexualized language or imagery, and sexual attention or advances of any kind
      • Trolling, insulting or derogatory comments, and personal or political attacks
      • Public or private harassment
      • Publishing others’ private information, such as a physical or email address, without their explicit permission
      • Other conduct which could reasonably be considered inappropriate in a professional setting
        • -
    + +
    -

    Enforcement Responsibilities

    +

    Enforcement Responsibilities +

    Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.

    Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.

    -

    Scope

    +

    Scope +

    This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.

    -

    Enforcement

    +

    Enforcement +

    Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at [INSERT CONTACT METHOD]. All complaints will be reviewed and investigated promptly and fairly.

    All community leaders are obligated to respect the privacy and security of the reporter of any incident.

    -

    Enforcement Guidelines

    +

    Enforcement Guidelines +

    Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:

    -

    1. Correction

    +

    1. Correction +

    Community Impact: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.

    Consequence: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.

    -

    2. Warning

    +

    2. Warning +

    Community Impact: A violation through a single incident or series of actions.

    Consequence: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.

    -

    3. Temporary Ban

    +

    3. Temporary Ban +

    Community Impact: A serious violation of community standards, including sustained inappropriate behavior.

    Consequence: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.

    -

    4. Permanent Ban

    +

    4. Permanent Ban +

    Community Impact: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.

    Consequence: A permanent ban from any sort of public interaction within the community.

    -

    Attribution

    +

    Attribution +

    This Code of Conduct is adapted from the Contributor Covenant, version 2.1, available at https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.

    Community Impact Guidelines were inspired by Mozilla’s code of conduct enforcement ladder.

    For answers to common questions about this code of conduct, see the FAQ at https://www.contributor-covenant.org/faq. Translations are available at https://www.contributor-covenant.org/translations.

    @@ -126,17 +161,19 @@

    Attribution

    + + + + - - + + diff --git a/v0.1.6/CONTRIBUTING.html b/v0.1.6/CONTRIBUTING.html index 8bbe79a3..2a20c6b3 100644 --- a/v0.1.6/CONTRIBUTING.html +++ b/v0.1.6/CONTRIBUTING.html @@ -1,8 +1,22 @@ - -Contribution Guidelines • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -62,7 +82,8 @@

    🙏 Thank you for taking the time to contribute!

    Your input is deeply valued, whether an issue, a pull request, or even feedback, regardless of size, content or scope.

    -

    Table of contents

    +

    Table of contents +

    👶 Getting started

    📔 Code of Conduct

    🗃 License

    @@ -73,38 +94,47 @@

    Table of contents❓ Questions

    -

    Getting started

    +

    Getting started +

    Please refer the project documentation for a brief introduction. Please also see other articles within the project documentation for additional information.

    -

    Code of Conduct

    +

    Code of Conduct +

    A Code of Conduct governs this project. Participants and contributors are expected to follow the rules outlined therein.

    -

    License

    +

    License +

    All your contributions will be covered by this project’s license.

    -

    Issues

    +

    Issues +

    We use GitHub to track issues, feature requests, and bugs. Before submitting a new issue, please check if the issue has already been reported. If the issue already exists, please upvote the existing issue 👍.

    For new feature requests, please elaborate on the context and the benefit the feature will have for users, developers, or other relevant personas.

    -

    Pull requests

    +

    Pull requests +

    -

    GitHub Flow

    +

    GitHub Flow +

    This repository uses the GitHub Flow model for collaboration. To submit a pull request:

    -
    1. +
        +

      1. Create a branch

        Please see the branch naming convention below. If you don’t have write access to this repository, please fork it.

      2. Make changes

        Make sure your code

        -
        • passes all checks imposed by GitHub Actions
          • +
            +
          • passes all checks imposed by GitHub Actions
          • is well documented
          • is well tested with unit tests sufficiently covering the changes introduced
            • -
          +
        +

      3. Create a pull request (PR)

        In the pull request description, please link the relevant issue (if any), provide a detailed description of the change, and include any assumptions.

        @@ -118,76 +148,93 @@

        GitHub Flow -

        Branch naming convention

        +

        Branch naming convention +

        Suppose your changes are related to a current issue in the current project; please name your branch as follows: <issue_id>_<short_description>. Please use underscore (_) as a delimiter for word separation. For example, 420_fix_ui_bug would be a suitable branch name if your change is resolving and UI-related bug reported in issue number 420 in the current project.

        If your change affects multiple repositories, please name your branches as follows: <issue_id>_<issue_repo>_<short description>. For example, 69_awesomeproject_fix_spelling_error would reference issue 69 reported in project awesomeproject and aims to resolve one or more spelling errors in multiple (likely related) repositories.

    monorepo and staged.dependencies -

    + +

    Sometimes you might need to change upstream dependent package(s) to be able to submit a meaningful change. We are using staged.dependencies functionality to simulate a monorepo behavior. The dependency configuration is already specified in this project’s staged_dependencies.yaml file. You need to name the feature branches appropriately. This is the only exception from the branch naming convention described above.

    Please refer to the staged.dependencies package documentation for more details.

    -

    Coding guidelines

    +

    Coding guidelines +

    This repository follows some unified processes and standards adopted by its maintainers to ensure software development is carried out consistently within teams and cohesively across other repositories.

    -

    Style guide

    +

    Style guide +

    This repository follows the standard tidyverse style guide and uses lintr for lint checks. Customized lint configurations are available in this repository’s .lintr file.

    -

    Dependency management

    +

    Dependency management +

    Lightweight is the right weight. This repository follows tinyverse recommedations of limiting dependencies to minimum.

    -

    Dependency version management

    +

    Dependency version management +

    If the code is not compatible with all (!) historical versions of a given dependenct package, it is required to specify minimal version in the DESCRIPTION file. In particular: if the development version requires (imports) the development version of another package - it is required to put abc (>= 1.2.3.9000).

    -

    Recommended development environment & tools

    +

    Recommended development environment & tools +

    -

    R & package versions

    +

    R & package versions +

    We continuously test our packages against the newest R version along with the most recent dependencies from CRAN and BioConductor. We recommend that your working environment is also set up in the same way. You can find the details about the R version and packages used in the R CMD check GitHub Action execution log - there is a step that prints out the R sessionInfo().

    If you discover bugs on older R versions or with an older set of dependencies, please create the relevant bug reports.

    -

    pre-commit

    +

    +pre-commit +

    We highly recommend that you use the pre-commit tool combined with R hooks for pre-commit to execute some of the checks before committing and pushing your changes.

    Pre-commit hooks are already available in this repository’s .pre-commit-config.yaml file.

    -

    Recognition model

    +

    Recognition model +

    As mentioned previously, all contributions are deeply valued and appreciated. While all contribution data is available as part of the repository insights, to recognize a significant contribution and hence add the contributor to the package authors list, the following rules are enforced:

    -
    • Minimum 5% of lines of code authored* (determined by git blame query) OR
      • +
        +
      • Minimum 5% of lines of code authored* (determined by git blame query) OR
      • Being at the top 5 contributors in terms of number of commits OR lines added OR lines removed*
        • -

      *Excluding auto-generated code, including but not limited to roxygen comments or renv.lock files.

      +
    +

    *Excluding auto-generated code, including but not limited to roxygen comments or renv.lock files.

    The package maintainer also reserves the right to adjust the criteria to recognize contributions.

    -

    Questions

    +

    Questions +

    If you have further questions regarding the contribution guidelines, please contact the package/repository maintainer.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/LICENSE-text.html b/v0.1.6/LICENSE-text.html index b423548f..85e691d9 100644 --- a/v0.1.6/LICENSE-text.html +++ b/v0.1.6/LICENSE-text.html @@ -1,8 +1,22 @@ - -License • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,17 +92,19 @@ limitations under the License. - + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/SECURITY.html b/v0.1.6/SECURITY.html index 8ca9c588..c6da2650 100644 --- a/v0.1.6/SECURITY.html +++ b/v0.1.6/SECURITY.html @@ -1,8 +1,22 @@ - -Security Policy • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -60,38 +80,44 @@
    -

    Reporting Security Issues

    +

    Reporting Security Issues +

    If you believe you have found a security vulnerability in any of the repositories in this organization, please report it to us through coordinated disclosure.

    Please do not report security vulnerabilities through public GitHub issues, discussions, or pull requests.

    Instead, please send an email to vulnerability.management[@]roche.com.

    Please include as much of the information listed below as you can to help us better understand and resolve the issue:

    -
    • The type of issue (e.g., buffer overflow, SQL injection, or cross-site scripting)
      • +
        +
      • The type of issue (e.g., buffer overflow, SQL injection, or cross-site scripting)
      • Full paths of source file(s) related to the manifestation of the issue
      • The location of the affected source code (tag/branch/commit or direct URL)
      • Any special configuration required to reproduce the issue
      • Step-by-step instructions to reproduce the issue
      • Proof-of-concept or exploit code (if possible)
      • Impact of the issue, including how an attacker might exploit the issue
        • -

      This information will help us triage your report more quickly.

      +
    +

    This information will help us triage your report more quickly.

    -

    Data Security Standards (DSS)

    +

    Data Security Standards (DSS) +

    Please make sure that while reporting issues in the form a bug, feature, or pull request, all sensitive information such as PII, PHI, and PCI is completely removed from any text and attachments, including pictures and videos.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/articles/Getting_Started.html b/v0.1.6/articles/Getting_Started.html index 2a32b1ea..7a27498e 100644 --- a/v0.1.6/articles/Getting_Started.html +++ b/v0.1.6/articles/Getting_Started.html @@ -1,5 +1,4 @@ - - + @@ -46,14 +45,15 @@ Changelog
  • -
    main + +
    + main latest-tag v0.1.6 v0.1.5 -v0.1.4
    • +v0.1.4 + + + + -
    • +
        +
        • -
      +
    + @@ -60,20 +80,25 @@

    All vignettes

    -
    Getting Started
    +
    +
    Getting Started
    -
    - + +
    + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/authors.html b/v0.1.6/authors.html index 88333e84..4564cea7 100644 --- a/v0.1.6/authors.html +++ b/v0.1.6/authors.html @@ -1,8 +1,22 @@ - -Authors and Citation • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -59,7 +79,8 @@

    Authors

    -
    • +
        +

      • Daniel Sabanés Bové. Author, maintainer.

        • @@ -127,7 +148,8 @@

        Authors

        F. Hoffmann-La Roche AG. Copyright holder, funder.

        -
    + +

    Citation

    @@ -148,17 +170,19 @@

    Citation

    }
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/index.html b/v0.1.6/index.html index 396804f3..4ab25fcd 100644 --- a/v0.1.6/index.html +++ b/v0.1.6/index.html @@ -1,5 +1,4 @@ - - + @@ -46,14 +45,15 @@ Changelog
  • -
    main + +
    + main latest-tag v0.1.6 v0.1.5 -v0.1.4
    • +v0.1.4 + + + + -
    • +
        +
        • -
      +
    + @@ -58,78 +78,119 @@
    -

    teal.modules.hermes 0.1.6

    +

    teal.modules.hermes 0.1.6 +

    -

    Miscellaneous

    -
    • Added placeholders for assaySpec, adtteSpec and geneSpec inputs when no option is selected.
      • +

      Miscellaneous +

      +
        +
      • Added placeholders for assaySpec, adtteSpec and geneSpec inputs when no option is selected.
      • Disabled the select input for assaySpec and adtteSpec when there are no options available.
      • For module developers: The module gets teal_data object in the UI and reactive(<teal_data>) in the server
        • -
    + +
    -

    Enhancements

    -
    • Updated the documentation and vignettes with the new way of specifying data for teal::init(). The data argument accepts teal_data object.
      • -
    +

    Enhancements +

    +
      +
    • Updated the documentation and vignettes with the new way of specifying data for teal::init(). The data argument accepts teal_data object.
      • +
    +
    -

    teal.modules.hermes 0.1.5

    +

    teal.modules.hermes 0.1.5 +

    -

    Bug Fixes

    -
    • Filtering data with the filter panel now correctly triggers the sampleVarSpecModule.
      • -
    +

    Bug Fixes +

    +
      +
    • Filtering data with the filter panel now correctly triggers the sampleVarSpecModule.
      • +
    +
    -

    Breaking changes

    -
    • Replaced datasets argument containing FilteredData with the new arguments data (tdata object) and filter_panel_api (FilterPanelAPI).
      • -
    +

    Breaking changes +

    +
      +
    • Replaced datasets argument containing FilteredData with the new arguments data (tdata object) and filter_panel_api (FilterPanelAPI).
      • +
    +
    -

    Miscellaneous

    -
    • Removed scda from dependencies.
      • +

      Miscellaneous +

      +
        +
      • Removed scda from dependencies.
      • Migrate to shinytest2.
        • -
    + +
    -

    teal.modules.hermes 0.1.4

    -
    • Added the teal.reporter functionality to all modules.
      • +

      teal.modules.hermes 0.1.4 +

      +
        +
      • Added the teal.reporter functionality to all modules.
      • Add installation instruction
        • -
    + +
    -

    teal.modules.hermes 0.1.3

    -
    • Improve the selection of sample variables in the forest module (tm_g_forest_tte) such that only categorical variables can be selected in the first place.
      • -
    -

    Miscellaneous

    -
    • Added a template to the pkgdown site.
      • +

      teal.modules.hermes 0.1.3 +

      +
        +
      • Improve the selection of sample variables in the forest module (tm_g_forest_tte) such that only categorical variables can be selected in the first place.
        • +
      +
      +

      Miscellaneous +

      +
        +
      • Added a template to the pkgdown site.
      • Updated package authors.
      • Added the option categorical_only to the sampleVarSpec server module, which allows to only show categorical sample variables for selection.
        • -
      +
    +
    -

    teal.modules.hermes 0.1.2

    -
    • Rewrote modules to use moduleServer and updated call to plot_with_settings_srv after changes in teal.devel.
      • +

      teal.modules.hermes 0.1.2 +

      +
        +
      • Rewrote modules to use moduleServer and updated call to plot_with_settings_srv after changes in teal.devel.
      • Replaced calls to teal::root_modules with teal::modules following deprecation of teal::root_modules.
      • Added basic logging to the modules.
      • Fixed the geneSpecInput so that the hermes app doesn’t fail anymore (on chrome) on an experiment with no genes.
        • -
    + +
    -

    teal.modules.hermes 0.1.1

    +

    teal.modules.hermes 0.1.1 +

    -

    Bug Fixes

    -
    • Updated legend for the PCA plot.
      • +

      Bug Fixes +

      +
        +
      • Updated legend for the PCA plot.
      • Gene selection with more than a few thousand genes no longer hangs the application. This is achieved through a different selection input in the corresponding geneSpec shiny module.
      • Only atomic columns of colData with at least one value can now be selected in the sampleVarSpecModule.
        • -
    + +
    -

    Miscellaneous

    -
    • Updated R version requirement to >= 3.6.
      • +

      Miscellaneous +

      +
        +
      • Updated R version requirement to >= 3.6.
      • Updated sampleVarSpec and geneSpec modules with new icons to remove warnings when using shiny version >= 1.7.
      • Removed dependencies on deprecated packages utils.nest and test.nest.
        • -
    + +
    -

    teal.modules.hermes 0.1.0

    -
    • First release of the teal.modules.hermes package, which contains teal modules for RNA-seq analysis using the hermes package.
      • +

      teal.modules.hermes 0.1.0 +

      +
        +
      • First release of the teal.modules.hermes package, which contains teal modules for RNA-seq analysis using the hermes package.
      • New users should first begin by reading the README.md of the teal.modules.hermes package to become familiar.
        • -
      -

      New Features

      -
      • +
      +
      +

      New Features +

      +
      +
    +
    + + + + - - + + diff --git a/v0.1.6/pull_request_template.html b/v0.1.6/pull_request_template.html index 576c50ff..8da717e2 100644 --- a/v0.1.6/pull_request_template.html +++ b/v0.1.6/pull_request_template.html @@ -1,8 +1,22 @@ - -Pull Request • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,17 +83,19 @@

    Fixes #nnn

    - + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/reference/adtteSpecInput.html b/v0.1.6/reference/adtteSpecInput.html index 878d6d91..43f5b3ae 100644 --- a/v0.1.6/reference/adtteSpecInput.html +++ b/v0.1.6/reference/adtteSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for ADTTE Specification — adtteSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,13 +88,16 @@
    -

    Usage

    +

    Usage +

    adtteSpecInput(inputId, label_paramcd = "Select Endpoint")
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -80,30 +105,35 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    adtteSpecServer() for the module server and a complete example.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/reference/adtteSpecServer.html b/v0.1.6/reference/adtteSpecServer.html index 868a9931..3457966c 100644 --- a/v0.1.6/reference/adtteSpecServer.html +++ b/v0.1.6/reference/adtteSpecServer.html @@ -1,18 +1,34 @@ - - + + + + + +Module Server for ADTTE Specification — adtteSpecServer • teal.modules.hermes +Module Server for ADTTE Specification — adtteSpecServer • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -28,7 +44,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -78,7 +100,8 @@
    -

    Usage

    +

    Usage +

    adtteSpecServer(
   id,
   data,
@@ -94,8 +117,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -115,8 +140,11 @@

    ArgumentsArgumentsArguments -

    Value

    +

    Value +

    -

    List with the following elements:

    • binned_adtte_subset: reactive containing the joined ADTTE and gene data.

      • +

      List with the following elements:

      +
        +

      • binned_adtte_subset: reactive containing the joined ADTTE and gene data.

      • gene_col: reactive containing the string with the column name of the original numeric gene variable.

      • gene_factor: string with the variable name for the binned gene data.

      • time_unit: reactive string with the time unit for the current subset.

        • -
    + +
    -

    See also

    +

    See also +

    adtteSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id) {
   ns <- NS(id)
 
@@ -260,17 +296,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/assaySpecInput.html b/v0.1.6/reference/assaySpecInput.html index 1d70983e..4369a34a 100644 --- a/v0.1.6/reference/assaySpecInput.html +++ b/v0.1.6/reference/assaySpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Assay Specification — assaySpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,13 +88,16 @@
    -

    Usage

    +

    Usage +

    assaySpecInput(inputId, label_assays = "Select Assay")
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -80,30 +105,35 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    assaySpecServer() for the module server and a complete example.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/reference/assaySpecServer.html b/v0.1.6/reference/assaySpecServer.html index 2f148680..8e1f92ca 100644 --- a/v0.1.6/reference/assaySpecServer.html +++ b/v0.1.6/reference/assaySpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Assay Specification — assaySpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,13 +88,16 @@
    -

    Usage

    +

    Usage +

    assaySpecServer(id, assays, exclude_assays = character())
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -84,20 +109,24 @@

    Arguments -

    Value

    +

    Value +

    The chosen assay as a reactive string.

    -

    See also

    +

    See also +

    assaySpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id) {
   ns <- NS(id)
   teal.widgets::standard_layout(
@@ -155,17 +184,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/assert_adtte_vars.html b/v0.1.6/reference/assert_adtte_vars.html index 1860e3f8..64afbbb7 100644 --- a/v0.1.6/reference/assert_adtte_vars.html +++ b/v0.1.6/reference/assert_adtte_vars.html @@ -1,10 +1,26 @@ - -Check for ADTTE Variables — assert_adtte_vars • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,38 +88,46 @@
    -

    Usage

    +

    Usage +

    assert_adtte_vars(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    -
    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    assert_adtte_vars(list(aval = "AV", is_event = "EV", paramcd = "PC", usubjid = "ID", avalu = "u"))
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/reference/assert_summary_funs.html b/v0.1.6/reference/assert_summary_funs.html index 859aa865..30570fe5 100644 --- a/v0.1.6/reference/assert_summary_funs.html +++ b/v0.1.6/reference/assert_summary_funs.html @@ -1,10 +1,26 @@ - -Check for List of Summary Functions — assert_summary_funs • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,13 +88,16 @@
    -

    Usage

    +

    Usage +

    assert_summary_funs(x, null.ok = FALSE)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    @@ -80,29 +105,34 @@

    Arguments -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    assert_summary_funs(list(mean = colMeans, raw = NULL), null.ok = TRUE)
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/reference/assertion_arguments.html b/v0.1.6/reference/assertion_arguments.html index a831d618..ec0081fd 100644 --- a/v0.1.6/reference/assertion_arguments.html +++ b/v0.1.6/reference/assertion_arguments.html @@ -1,10 +1,26 @@ - -Standard Assertion Arguments — assertion_arguments • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -67,8 +89,10 @@
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    @@ -95,19 +119,22 @@

    Argumentscheckmate::vname().

    -

    + + - + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/reference/assertions.html b/v0.1.6/reference/assertions.html index cc5385df..665dc153 100644 --- a/v0.1.6/reference/assertions.html +++ b/v0.1.6/reference/assertions.html @@ -1,14 +1,30 @@ - - + + + + + +Additional Assertions for checkmate — assertions • teal.modules.hermes +Additional Assertions for checkmate — assertions • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    +
    -

    Additional Assertions for checkmate

    +

    Additional Assertions for checkmate +

    Source: R/checkmate.R
    assertions.Rd
    @@ -73,32 +96,39 @@
    -

    Value

    +

    Value +

    -

    Depending on the function prefix.

    • assert_ functions return the object invisibly if successful, and otherwise +

      Depending on the function prefix.

      +
        +

      • assert_ functions return the object invisibly if successful, and otherwise throw an error message.

      • check_ functions return TRUE if successful, otherwise a string with the error message.

      • test_ functions just return TRUE or FALSE.

        • -
    + +
    -

    See also

    +

    See also +

    assert_tag(), assert_reactive(), assert_summary_funs(), assert_adtte_vars()

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/reference/check_reactive.html b/v0.1.6/reference/check_reactive.html index fbb86217..bb9c8783 100644 --- a/v0.1.6/reference/check_reactive.html +++ b/v0.1.6/reference/check_reactive.html @@ -1,10 +1,26 @@ - -Check for Reactive Input — check_reactive • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    check_reactive(x)
 
 assert_reactive(x, .var.name = checkmate::vname(x), add = NULL)
@@ -75,8 +98,10 @@ 
    Usage
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    @@ -89,14 +114,17 @@

    Argumentscheckmate::AssertCollection.

    -

    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    check_reactive("bla")
 #> [1] FALSE
 check_reactive(reactive("bla"))
@@ -104,17 +132,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/check_tag.html b/v0.1.6/reference/check_tag.html index a1facee1..9e42b418 100644 --- a/v0.1.6/reference/check_tag.html +++ b/v0.1.6/reference/check_tag.html @@ -1,10 +1,26 @@ - -Check for Shiny Tag — check_tag • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    check_tag(x, null.ok = FALSE)
 
 assert_tag(x, null.ok = FALSE, .var.name = checkmate::vname(x), add = NULL)
@@ -77,8 +100,10 @@ 
    Usage
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    an object to check.

    @@ -105,14 +130,17 @@

    Argumentscheckmate::vname().

    -

    + +
    -

    See also

    +

    See also +

    assertions for more details.

    -

    Examples

    +

    Examples +

    check_tag("bla")
 #> [1] "Must be a 'shiny.tag' or NULL"
 check_tag(NULL, null.ok = TRUE)
@@ -120,17 +148,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/experimentSpecInput.html b/v0.1.6/reference/experimentSpecInput.html index f26a31ed..9ed6808e 100644 --- a/v0.1.6/reference/experimentSpecInput.html +++ b/v0.1.6/reference/experimentSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Experiment Specification — experimentSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    experimentSpecInput(
   inputId,
   data,
@@ -76,8 +99,10 @@ 
    Usage
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -95,30 +120,35 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    experimentSpecServer() for the module server and a complete example.

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/reference/experimentSpecServer.html b/v0.1.6/reference/experimentSpecServer.html index 4e7f4fc1..a4ea71b2 100644 --- a/v0.1.6/reference/experimentSpecServer.html +++ b/v0.1.6/reference/experimentSpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Experiment Specification — experimentSpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    experimentSpecServer(
   id,
   data,
@@ -79,8 +102,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -113,23 +138,30 @@

    Arguments -

    Value

    +

    Value +

    -

    List with the following reactive objects:

    • data: the hermes::AnyHermesData experiment.

      • +

      List with the following reactive objects:

      +
        +

      • data: the hermes::AnyHermesData experiment.

      • name: the name of the experiment as selected by the user.

      • genes: a data.frame with the genes in data, with columns id and name.

      • assays: the names of the assays in data.

        • -
    + +
    -

    See also

    +

    See also +

    experimentSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id,
                mae_name) {
   ns <- NS(id)
@@ -211,17 +243,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/function_arguments.html b/v0.1.6/reference/function_arguments.html index 7532e036..ddbb5ef5 100644 --- a/v0.1.6/reference/function_arguments.html +++ b/v0.1.6/reference/function_arguments.html @@ -1,10 +1,26 @@ - -Standard Function Arguments — function_arguments • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -67,8 +89,10 @@
    -

    Arguments

    -
    adtte
    +

    Arguments +

    +
    +
    adtte

    (data frame)
    an adtte dataset.

    @@ -96,19 +120,22 @@

    Arguments

    teal.modules.hermes is a part of the NEST and pharmaverse.

    - + + - - + + diff --git a/v0.1.6/reference/geneSpecInput.html b/v0.1.6/reference/geneSpecInput.html index b4762ece..d6a48b9b 100644 --- a/v0.1.6/reference/geneSpecInput.html +++ b/v0.1.6/reference/geneSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Gene Signature Specification — geneSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    geneSpecInput(
   inputId,
   funs,
@@ -83,8 +106,10 @@ 
    Usage
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -126,20 +151,24 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    geneSpecServer() for the module server and a complete example.

    -

    Examples

    +

    Examples +

    geneSpecInput("my_genes", list(mean = colMeans), label_funs = "Please select function")
 #> <div class="row">
 #>   <div class="col-sm-8">
@@ -205,17 +234,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/geneSpecServer.html b/v0.1.6/reference/geneSpecServer.html index df102e7f..ca698ce9 100644 --- a/v0.1.6/reference/geneSpecServer.html +++ b/v0.1.6/reference/geneSpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Gene Signature Specification — geneSpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    geneSpecServer(
   id,
   funs,
@@ -78,8 +101,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -100,21 +125,25 @@

    Arguments -

    Value

    +

    Value +

    Reactive hermes::GeneSpec which can be used as input for the relevant hermes functions.

    -

    See also

    +

    See also +

    geneSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id, funs) {
   ns <- NS(id)
   teal.widgets::standard_layout(
@@ -184,17 +213,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/h_assign_to_group_list.html b/v0.1.6/reference/h_assign_to_group_list.html index 9063676f..99370c98 100644 --- a/v0.1.6/reference/h_assign_to_group_list.html +++ b/v0.1.6/reference/h_assign_to_group_list.html @@ -1,12 +1,28 @@ - - + + + + + +Helper Function For Group List Creation — h_assign_to_group_list • teal.modules.hermes +Helper Function For Group List Creation — h_assign_to_group_list • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,25 +91,31 @@
    -

    Usage

    +

    Usage +

    h_assign_to_group_list(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (named list of character)
    input assignment list.

    -
    + +
    -

    Value

    +

    Value +

    A combination list.

    -

    Examples

    +

    Examples +

    assign_list <- list(
   "ASIAN" = "1",
   "BLACK OR AFRICAN AMERICAN" = "1",
@@ -105,17 +133,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/h_collapse_levels.html b/v0.1.6/reference/h_collapse_levels.html index ebb61723..17a85628 100644 --- a/v0.1.6/reference/h_collapse_levels.html +++ b/v0.1.6/reference/h_collapse_levels.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function for Collapsing of Factor Levels — h_collapse_levels • teal.modules.hermes +Helper Function for Collapsing of Factor Levels — h_collapse_levels • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,13 +94,16 @@
    -

    Usage

    +

    Usage +

    h_collapse_levels(x, group_list)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (factor)
    original factor.

    @@ -86,16 +111,19 @@

    Arguments -

    Value

    +

    Value +

    The transformed factor x with new levels.

    -

    Examples

    +

    Examples +

    set.seed(123)
 x <- factor(sample(
   c("ASIAN", "BLACK OR AFRICAN AMERICAN", "MULTIPLE", "UNKNOWN", "WHITE"),
@@ -112,17 +140,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/h_extract_words.html b/v0.1.6/reference/h_extract_words.html index af36d3f9..49c91294 100644 --- a/v0.1.6/reference/h_extract_words.html +++ b/v0.1.6/reference/h_extract_words.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Extract Words — h_extract_words • teal.modules.hermes +Helper Function to Extract Words — h_extract_words • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,25 +94,31 @@
    -

    Usage

    +

    Usage +

    h_extract_words(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (string)
    input.

    -
    + +
    -

    Value

    +

    Value +

    Character vector with the extracted words.

    -

    Examples

    +

    Examples +

    h_extract_words("a, b, , c, 234; 34562 - GeneID:bla")
 #> [1] "a"          "b"          "c"          "234"        "34562"     
 #> [6] "GeneID:bla"
@@ -99,17 +127,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/h_gene_data.html b/v0.1.6/reference/h_gene_data.html index 3e91f4b8..cb85deb2 100644 --- a/v0.1.6/reference/h_gene_data.html +++ b/v0.1.6/reference/h_gene_data.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Format Gene Choices — h_gene_data • teal.modules.hermes +Helper Function to Format Gene Choices — h_gene_data • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,13 +94,16 @@
    -

    Usage

    +

    Usage +

    h_gene_data(object, name_annotation)
    -

    Arguments

    -
    object
    +

    Arguments +

    +
    +
    object

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    @@ -87,23 +112,27 @@

    Arguments -

    Value

    +

    Value +

    A data.frame with id and name columns containing all genes from object.

    -

    Details

    +

    Details +

    Note that missing names or names that only contain whitespace are replaced by empty strings for consistency and better labeling in the UI downstream

    -

    Examples

    +

    Examples +

    object <- hermes::hermes_data[1:10, ]
 h_gene_data(object, "symbol")
 #>                  id         name
@@ -120,17 +149,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/h_km_mae_to_adtte.html b/v0.1.6/reference/h_km_mae_to_adtte.html index c1154486..fefb036a 100644 --- a/v0.1.6/reference/h_km_mae_to_adtte.html +++ b/v0.1.6/reference/h_km_mae_to_adtte.html @@ -1,10 +1,26 @@ - -Data Preprocessing for ADTTE Module — h_km_mae_to_adtte • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    h_km_mae_to_adtte(
   adtte,
   mae,
@@ -78,8 +101,10 @@ 
    Usage
    -

    Arguments

    -
    adtte
    +

    Arguments +

    +
    +
    adtte

    (data frame)
    an adtte dataset.

    @@ -103,9 +128,11 @@

    Arguments -

    Value

    +

    Value +

    A data frame containing all columns/rows from adtte that match @@ -114,13 +141,15 @@

    Value

    -

    Note

    +

    Note +

    The final gene column names can start with a different string than the original gene IDs (or labels), in particular white space and colons are removed.

    -

    Examples

    +

    Examples +

    mae <- hermes::multi_assay_experiment
 adtte <- teal.modules.hermes::rADTTE %>%
   dplyr::mutate(CNSR = as.logical(CNSR))
@@ -146,17 +175,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/h_order_genes.html b/v0.1.6/reference/h_order_genes.html index f70fccd2..20eab4de 100644 --- a/v0.1.6/reference/h_order_genes.html +++ b/v0.1.6/reference/h_order_genes.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Order Gene Choices — h_order_genes • teal.modules.hermes +Helper Function to Order Gene Choices — h_order_genes • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,26 +94,32 @@
    -

    Usage

    +

    Usage +

    h_order_genes(genes)
    -

    Arguments

    -
    genes
    +

    Arguments +

    +
    +
    genes

    (data.frame)
    containing id and name columns of the gene choices. Note that no missing values are allowed.

    -
    + +
    -

    Value

    +

    Value +

    The ordered data.frame.

    -

    Examples

    +

    Examples +

    genes <- data.frame(
   id = c("7", "1", "2", "345346", "0"),
   name = c("e", "", "c", "", "a")
@@ -106,17 +134,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/h_parse_genes.html b/v0.1.6/reference/h_parse_genes.html index eb7c7b8a..6acab47a 100644 --- a/v0.1.6/reference/h_parse_genes.html +++ b/v0.1.6/reference/h_parse_genes.html @@ -1,12 +1,28 @@ - - + + + + + +Helper Function to Parse Genes — h_parse_genes • teal.modules.hermes +Helper Function to Parse Genes — h_parse_genes • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,13 +91,16 @@
    -

    Usage

    +

    Usage +

    h_parse_genes(words, choices)
    -

    Arguments

    -
    words
    +

    Arguments +

    +
    +
    words

    (character)
    containing gene IDs or names.

    @@ -83,16 +108,19 @@

    Arguments -

    Value

    +

    Value +

    The subset of choices which matches words in ID or name.

    -

    Examples

    +

    Examples +

    h_parse_genes(
   c("a", "2535"),
   data.frame(id = as.character(2533:2537), name = letters[1:5])
@@ -103,17 +131,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/h_update_gene_selection.html b/v0.1.6/reference/h_update_gene_selection.html index 2222c383..9232dc67 100644 --- a/v0.1.6/reference/h_update_gene_selection.html +++ b/v0.1.6/reference/h_update_gene_selection.html @@ -1,14 +1,30 @@ - - + + + + + +Helper Function to Update Gene Selection — h_update_gene_selection • teal.modules.hermes +Helper Function to Update Gene Selection — h_update_gene_selection • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,13 +94,16 @@
    -

    Usage

    +

    Usage +

    h_update_gene_selection(session, inputId, selected, choices)
    -

    Arguments

    -
    session
    +

    Arguments +

    +
    +
    session

    (ShinySession)
    the session object.

    @@ -95,20 +120,23 @@

    Arguments

    + + + + - - + + diff --git a/v0.1.6/reference/heatmap_plot.html b/v0.1.6/reference/heatmap_plot.html index 89300972..2ab14d2c 100644 --- a/v0.1.6/reference/heatmap_plot.html +++ b/v0.1.6/reference/heatmap_plot.html @@ -1,10 +1,26 @@ - -Correlation Heatmap Plot — heatmap_plot • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,29 +88,35 @@
    -

    Usage

    +

    Usage +

    heatmap_plot(object, assay_name)
    -

    Arguments

    -
    object
    +

    Arguments +

    +
    +
    object

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    assay_name

    (string)
    the assay to define the groups.

    -
    + +
    -

    Value

    +

    Value +

    Plot to be displayed in the teal app.

    -

    Examples

    +

    Examples +

    library(hermes)
 #> Loading required package: ggfortify
 #> Loading required package: SummarizedExperiment
@@ -164,17 +192,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/include_css_files.html b/v0.1.6/reference/include_css_files.html index c28212b2..5546230c 100644 --- a/v0.1.6/reference/include_css_files.html +++ b/v0.1.6/reference/include_css_files.html @@ -1,12 +1,28 @@ - - + + + + + +Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.modules.hermes +Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,35 +91,42 @@
    -

    Usage

    +

    Usage +

    include_css_files(pattern = "*")
    -

    Arguments

    -
    pattern
    +

    Arguments +

    +
    +
    pattern

    (character) pattern of files to be included

    -
    + +
    -

    Value

    +

    Value +

    HTML code that includes CSS files

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/reference/include_js_files.html b/v0.1.6/reference/include_js_files.html index 9b8268d6..5b5e3d4d 100644 --- a/v0.1.6/reference/include_js_files.html +++ b/v0.1.6/reference/include_js_files.html @@ -1,12 +1,28 @@ - - + + + + + +Include JS files from /inst/js/ package directory to application header — include_js_files • teal.modules.hermes +Include JS files from /inst/js/ package directory to application header — include_js_files • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,39 +91,46 @@
    -

    Usage

    +

    Usage +

    include_js_files(pattern = "*")
    -

    Arguments

    -
    pattern
    +

    Arguments +

    +
    +
    pattern

    (character) pattern of files to be included, passed to system.file

    except

    (character) vector of basename filenames to be excluded

    -
    + +
    -

    Value

    +

    Value +

    HTML code that includes JS files

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/reference/index.html b/v0.1.6/reference/index.html index 48989a39..f75b5cbc 100644 --- a/v0.1.6/reference/index.html +++ b/v0.1.6/reference/index.html @@ -1,8 +1,22 @@ - -Function reference • teal.modules.hermes + + + + + + + Skip to contents @@ -18,7 +32,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -57,280 +77,377 @@
    -

    Package

    +

    Package +

    -
    +
    +
    -
    +
    +
    teal.modules.hermes teal.modules.hermes-package
    -
    teal.modules.hermes Package
    -
    -

    Utility Functions

    +
    +teal.modules.hermes Package
    + +
    +
    +

    Utility Functions +

    -
    +
    +
    -
    +
    +
    h_assign_to_group_list()
    Helper Function For Group List Creation
    -
    +
    +
    +
    h_collapse_levels()
    Helper Function for Collapsing of Factor Levels
    -
    +
    +
    +
    h_extract_words()
    Helper Function to Extract Words
    -
    +
    +
    +
    h_gene_data()
    Helper Function to Format Gene Choices
    -
    +
    +
    +
    h_km_mae_to_adtte()
    Data Preprocessing for ADTTE Module
    -
    +
    +
    +
    h_order_genes()
    Helper Function to Order Gene Choices
    -
    +
    +
    +
    h_parse_genes()
    Helper Function to Parse Genes
    -
    +
    +
    +
    h_update_gene_selection()
    Helper Function to Update Gene Selection
    -
    +
    +
    +
    is_blank()
    Checking for Empty String
    -
    -

    Shiny Modules

    + +
    +
    +

    Shiny Modules +

    -
    +
    +
    -
    +
    +
    adtteSpecInput()
    Module Input for ADTTE Specification
    -
    +
    +
    +
    adtteSpecServer()
    Module Server for ADTTE Specification
    -
    +
    +
    +
    assaySpecInput()
    Module Input for Assay Specification
    -
    +
    +
    +
    assaySpecServer()
    Module Server for Assay Specification
    -
    +
    +
    +
    experimentSpecInput()
    Module Input for Experiment Specification
    -
    +
    +
    +
    experimentSpecServer()
    Module Server for Experiment Specification
    -
    +
    +
    +
    geneSpecInput()
    Module Input for Gene Signature Specification
    -
    +
    +
    +
    geneSpecServer()
    Module Server for Gene Signature Specification
    -
    +
    +
    +
    sampleVarSpecInput()
    Module Input for Sample Variable Specification
    -
    +
    +
    +
    sampleVarSpecServer()
    Module Server for Sample Variable Specification
    -
    +
    +
    +
    multiSampleVarSpecServer()
    Module Server for Specification of Multiple Sample Variables
    -
    -

    Teal Module Functions

    + +
    +
    +

    Teal Module Functions +

    -
    +
    +
    -
    +
    +
    tm_g_barplot() ui_g_barplot() srv_g_barplot() sample_tm_g_barplot()
    Teal Module for RNA-seq Barplot
    -
    +
    +
    +
    tm_g_boxplot() ui_g_boxplot() srv_g_boxplot() sample_tm_g_boxplot()
    Teal Module for RNA-seq Boxplot
    -
    +
    +
    +
    tm_g_forest_tte() ui_g_forest_tte() srv_g_forest_tte() sample_tm_g_forest_tte()
    Teal Module for Survival Forest Plot
    -
    +
    +
    +
    tm_g_km() ui_g_km() srv_g_km() sample_tm_g_km()
    Teal Module for Kaplan-Meier Plot
    -
    +
    +
    +
    tm_g_pca() ui_g_pca() srv_g_pca() sample_tm_g_pca()
    Teal Module for PCA Analysis
    -
    +
    +
    +
    tm_g_quality() ui_g_quality() srv_g_quality() sample_tm_g_quality()
    Teal Module for RNA-seq Quality Control
    -
    +
    +
    +
    tm_g_scatterplot() ui_g_scatterplot() srv_g_scatterplot() sample_tm_g_scatterplot()
    Teal Module for RNA-seq Scatterplot
    -
    +
    +
    +
    tm_g_volcanoplot() ui_g_volcanoplot() srv_g_volcanoplot() sample_tm_g_volcanoplot()
    Teal Module for RNA-seq Volcano Plot
    -
    -

    Graph Functions

    + +
    +
    +

    Graph Functions +

    -
    +
    +
    -
    +
    +
    heatmap_plot()
    Correlation Heatmap Plot
    -
    +
    +
    +
    top_gene_plot()
    Most Expressed Genes Plot
    -
    -

    Assertions

    + +
    +
    +

    Assertions +

    -
    +
    +
    -
    +
    +
    assert_adtte_vars()
    Check for ADTTE Variables
    -
    +
    +
    +
    check_reactive() assert_reactive() test_reactive()
    Check for Reactive Input
    -
    +
    +
    +
    assert_summary_funs()
    Check for List of Summary Functions
    -
    +
    +
    +
    check_tag() assert_tag() test_tag() expect_tag()
    Check for Shiny Tag
    -
    -

    Validations

    + +
    +
    +

    Validations +

    -
    +
    +
    -
    +
    +
    validate_gene_spec()
    Validation of Gene Specification
    -
    +
    +
    +
    validate_n_levels()
    Validation of Number of Levels
    -
    + + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/reference/is_blank.html b/v0.1.6/reference/is_blank.html index 504fdbd9..0218ae9e 100644 --- a/v0.1.6/reference/is_blank.html +++ b/v0.1.6/reference/is_blank.html @@ -1,12 +1,28 @@ - - + + + + + +Checking for Empty String — is_blank • teal.modules.hermes +Checking for Empty String — is_blank • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,25 +91,31 @@
    -

    Usage

    +

    Usage +

    is_blank(x)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    object to check.

    -
    + +
    -

    Value

    +

    Value +

    Flag whether x is identical to an empty string, i.e. "".

    -

    Examples

    +

    Examples +

    is_blank("")
 #> [1] TRUE
 is_blank(" ")
@@ -95,17 +123,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/module_arguments.html b/v0.1.6/reference/module_arguments.html index f92a768c..f250fde2 100644 --- a/v0.1.6/reference/module_arguments.html +++ b/v0.1.6/reference/module_arguments.html @@ -1,10 +1,26 @@ - -Standard Module Arguments — module_arguments • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -67,8 +89,10 @@
    -

    Arguments

    -
    data
    +

    Arguments +

    +
    +
    data

    (reactive)
    reactive(<teal_data>) holding all the data sets provided during app initialization after going through the filters.

    @@ -89,8 +113,11 @@

    ArgumentsArgumentsArguments

    teal.modules.hermes is a part of the NEST and pharmaverse.

    - + + - - + + diff --git a/v0.1.6/reference/multiSampleVarSpecServer.html b/v0.1.6/reference/multiSampleVarSpecServer.html index a4dd3341..b5b864d9 100644 --- a/v0.1.6/reference/multiSampleVarSpecServer.html +++ b/v0.1.6/reference/multiSampleVarSpecServer.html @@ -1,12 +1,28 @@ - - + + + + + +Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer • teal.modules.hermes +Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,13 +91,16 @@
    -

    Usage

    +

    Usage +

    multiSampleVarSpecServer(inputIds, original_data, ...)
    -

    Arguments

    -
    inputIds
    +

    Arguments +

    +
    +
    inputIds

    (character)
    multiple input IDs corresponding to the different sample variables specified in the UI function.

    @@ -93,9 +118,11 @@

    Arguments -

    Value

    +

    Value +

    List with the final transformed experiment_data reactive and a @@ -104,7 +131,8 @@

    Value

    -

    Examples

    +

    Examples +

    if (FALSE) {
 # In the server use:
 sample_var_specs <- multiSampleVarSpecServer(
@@ -122,17 +150,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/rADTTE.html b/v0.1.6/reference/rADTTE.html index 473a496b..938c0d8e 100644 --- a/v0.1.6/reference/rADTTE.html +++ b/v0.1.6/reference/rADTTE.html @@ -1,8 +1,24 @@ - -Random Time to Event Analysis Dataset — rADTTE • teal.modules.hermes + + + + + + + + Skip to contents @@ -18,7 +34,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -63,31 +85,36 @@
    -

    Usage

    +

    Usage +

    rADTTE
    -

    Format

    +

    Format +

    An object of class tbl_df (inherits from tbl, data.frame) with 2000 rows and 67 columns.

    -

    Source

    +

    Source +

    internal

    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/reference/sampleVarSpecInput.html b/v0.1.6/reference/sampleVarSpecInput.html index cbd6fc77..6a611c1f 100644 --- a/v0.1.6/reference/sampleVarSpecInput.html +++ b/v0.1.6/reference/sampleVarSpecInput.html @@ -1,10 +1,26 @@ - -Module Input for Sample Variable Specification — sampleVarSpecInput • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    sampleVarSpecInput(
   inputId,
   label_vars = "Select sample variable",
@@ -75,8 +98,10 @@ 
    Usage
    -

    Arguments

    -
    inputId
    +

    Arguments +

    +
    +
    inputId

    (string)
    the ID used to call the module input.

    @@ -88,20 +113,24 @@

    Arguments -

    Value

    +

    Value +

    The UI part.

    -

    See also

    +

    See also +

    sampleVarSpecServer() for the module server and a complete example.

    -

    Examples

    +

    Examples +

    sampleVarSpecInput("my_vars", label_vars = "Select faceting variable")
 #> <div class="row">
 #>   <div class="col-sm-8">
@@ -141,17 +170,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/sampleVarSpecServer.html b/v0.1.6/reference/sampleVarSpecServer.html index 8e9ea80b..5d102a7a 100644 --- a/v0.1.6/reference/sampleVarSpecServer.html +++ b/v0.1.6/reference/sampleVarSpecServer.html @@ -1,10 +1,26 @@ - -Module Server for Sample Variable Specification — sampleVarSpecServer • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    sampleVarSpecServer(
   id,
   experiment_name,
@@ -81,8 +104,10 @@ 
    Usage
    -

    Arguments

    -
    id
    +

    Arguments +

    +
    +
    id

    (string) the shiny module id.

    @@ -125,27 +150,32 @@

    Arguments -

    Value

    +

    Value +

    Reactive SummarizedExperiment::SummarizedExperiment which can be used as input for the relevant hermes functions.

    -

    Note

    +

    Note +

    Only atomic columns (e.g. not DataFrame columns) of the colData which are not completely missing (NA) will be shown for selection. If num_levels is specified then only factor columns will be available.

    -

    See also

    +

    See also +

    sampleVarSpecInput() for the module UI.

    -

    Examples

    +

    Examples +

    ui <- function(id) {
   checkmate::assert_class(data, "teal_data")
   ns <- NS(id)
@@ -216,17 +246,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/teal.modules.hermes-package.html b/v0.1.6/reference/teal.modules.hermes-package.html index 5a7c7fa5..a0d0a84c 100644 --- a/v0.1.6/reference/teal.modules.hermes-package.html +++ b/v0.1.6/reference/teal.modules.hermes-package.html @@ -1,10 +1,26 @@ - -teal.modules.hermes Package — teal.modules.hermes-package • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    +
    -

    teal.modules.hermes Package

    +

    +teal.modules.hermes Package

    Source: R/package.R
    teal.modules.hermes-package.Rd
    @@ -67,16 +90,24 @@
    -

    See also

    -

    Useful links:

    +
    -

    Author

    +

    Author +

    Maintainer: Daniel Sabanés Bové daniel.sabanes_bove@roche.com

    -

    Authors:

    • Nikolas Burkoff

      • +

      Authors:

      +
        +

      • Nikolas Burkoff

      • Dinakar Kulkarni

      • Konrad Pagacz

      • Namrata Bhatia

        • @@ -86,26 +117,32 @@

        Author<

      • Stefanie Bienert

      • Haocheng Li

      • Lyndsee Midori Zhang

        • -

      Other contributors:

      • Sorin Voicu [contributor]

        • +
      +

      Other contributors:

      +
        +

      • Sorin Voicu [contributor]

      • Benoit Falquet [contributor]

      • Mahmoud Hallal [contributor]

      • Tim Treis [contributor]

      • Vedha Viyash [contributor]

      • F. Hoffmann-La Roche AG [copyright holder, funder]

        • -
    + +
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/reference/tm_g_barplot.html b/v0.1.6/reference/tm_g_barplot.html index c9c7b301..578ecf2c 100644 --- a/v0.1.6/reference/tm_g_barplot.html +++ b/v0.1.6/reference/tm_g_barplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Barplot — tm_g_barplot • teal.modules.hermes +Teal Module for RNA-seq Barplot — tm_g_barplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_barplot(
   label,
   mae_name,
@@ -96,8 +119,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -145,23 +170,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_barplot(): sets up the user interface.

      • +
        +

      • ui_g_barplot(): sets up the user interface.

      • srv_g_barplot(): sets up the server with reactive graph.

      • sample_tm_g_barplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -184,17 +215,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/tm_g_boxplot.html b/v0.1.6/reference/tm_g_boxplot.html index 1a24f72b..8478cb54 100644 --- a/v0.1.6/reference/tm_g_boxplot.html +++ b/v0.1.6/reference/tm_g_boxplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Boxplot — tm_g_boxplot • teal.modules.hermes +Teal Module for RNA-seq Boxplot — tm_g_boxplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_boxplot(
   label,
   mae_name,
@@ -96,8 +119,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -145,23 +170,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_boxplot(): sets up the user interface.

      • +
        +

      • ui_g_boxplot(): sets up the user interface.

      • srv_g_boxplot(): sets up the server with reactive graph.

      • sample_tm_g_boxplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -184,17 +215,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/tm_g_forest_tte.html b/v0.1.6/reference/tm_g_forest_tte.html index cc7b84e6..747c05d4 100644 --- a/v0.1.6/reference/tm_g_forest_tte.html +++ b/v0.1.6/reference/tm_g_forest_tte.html @@ -1,10 +1,26 @@ - -Teal Module for Survival Forest Plot — tm_g_forest_tte • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,7 +88,8 @@
    -

    Usage

    +

    Usage +

    tm_g_forest_tte(
   label,
   adtte_name,
@@ -109,8 +132,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -126,8 +151,11 @@

    ArgumentsArgumentsArguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_forest_tte(): sets up the user interface.

      • +
        +

      • ui_g_forest_tte(): sets up the user interface.

      • srv_g_forest_tte(): sets up the server with reactive graph.

      • sample_tm_g_forest_tte(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data()
 data <- within(data, {
   ADTTE <- teal.modules.hermes::rADTTE %>%
@@ -235,17 +270,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/tm_g_km.html b/v0.1.6/reference/tm_g_km.html index 2c157c41..935e3a74 100644 --- a/v0.1.6/reference/tm_g_km.html +++ b/v0.1.6/reference/tm_g_km.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for Kaplan-Meier Plot — tm_g_km • teal.modules.hermes +Teal Module for Kaplan-Meier Plot — tm_g_km • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_km(
   label,
   adtte_name,
@@ -101,8 +124,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -118,8 +143,11 @@

    ArgumentsArgumentsArguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_km(): sets up the user interface.

      • +
        +

      • ui_g_km(): sets up the user interface.

      • srv_g_km(): sets up the user interface.

      • sample_tm_g_km(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data()
 data <- within(data, {
   ADTTE <- teal.modules.hermes::rADTTE %>%
@@ -221,17 +256,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/tm_g_pca.html b/v0.1.6/reference/tm_g_pca.html index d55d9368..d4885190 100644 --- a/v0.1.6/reference/tm_g_pca.html +++ b/v0.1.6/reference/tm_g_pca.html @@ -1,14 +1,30 @@ - - + + + + + +Teal Module for PCA Analysis — tm_g_pca • teal.modules.hermes +Teal Module for PCA Analysis — tm_g_pca • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,7 +94,8 @@
    -

    Usage

    +

    Usage +

    tm_g_pca(
   label,
   mae_name,
@@ -89,8 +112,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -132,23 +157,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_pca(): sets up the user interface.

      • +
        +

      • ui_g_pca(): sets up the user interface.

      • srv_g_pca(): sets up the server with reactive graph.

      • sample_tm_g_pca(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -171,17 +202,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/tm_g_quality.html b/v0.1.6/reference/tm_g_quality.html index 222430a5..3a7b7232 100644 --- a/v0.1.6/reference/tm_g_quality.html +++ b/v0.1.6/reference/tm_g_quality.html @@ -1,14 +1,30 @@ - - + + + + + +Teal Module for RNA-seq Quality Control — tm_g_quality • teal.modules.hermes +Teal Module for RNA-seq Quality Control — tm_g_quality • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -24,7 +40,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -72,7 +94,8 @@
    -

    Usage

    +

    Usage +

    tm_g_quality(
   label,
   mae_name,
@@ -89,8 +112,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -132,23 +157,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_quality(): sets up the user interface.

      • +
        +

      • ui_g_quality(): sets up the user interface.

      • srv_g_quality(): sets up the server with reactive graphs.

      • sample_tm_g_quality(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -170,17 +201,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/tm_g_scatterplot.html b/v0.1.6/reference/tm_g_scatterplot.html index f11189c6..cbb7a0b1 100644 --- a/v0.1.6/reference/tm_g_scatterplot.html +++ b/v0.1.6/reference/tm_g_scatterplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Scatterplot — tm_g_scatterplot • teal.modules.hermes +Teal Module for RNA-seq Scatterplot — tm_g_scatterplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_scatterplot(
   label,
   mae_name,
@@ -96,8 +119,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -145,23 +170,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_scatterplot(): sets up the user interface.

      • +
        +

      • ui_g_scatterplot(): sets up the user interface.

      • srv_g_scatterplot(): sets up the server with reactive graph.

      • sample_tm_g_scatterplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -184,17 +215,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/tm_g_volcanoplot.html b/v0.1.6/reference/tm_g_volcanoplot.html index 51b4f97f..e6f185bd 100644 --- a/v0.1.6/reference/tm_g_volcanoplot.html +++ b/v0.1.6/reference/tm_g_volcanoplot.html @@ -1,12 +1,28 @@ - - + + + + + +Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot • teal.modules.hermes +Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,7 +91,8 @@
    -

    Usage

    +

    Usage +

    tm_g_volcanoplot(
   label,
   mae_name,
@@ -93,8 +116,10 @@ 
    Usage
    -

    Arguments

    -
    label
    +

    Arguments +

    +
    +
    label

    (string)
    menu item label of the module in the teal app.

    @@ -136,23 +161,29 @@

    Arguments -

    Value

    +

    Value +

    Shiny module to be used in the teal app.

    -

    Functions

    +

    Functions +

    -

    • ui_g_volcanoplot(): sets up the user interface.

      • +
        +

      • ui_g_volcanoplot(): sets up the user interface.

      • srv_g_volcanoplot(): sets up the server with reactive graph.

      • sample_tm_g_volcanoplot(): sample module function.

        • -
    + +
    -

    Examples

    +

    Examples +

    data <- teal_data(MAE = hermes::multi_assay_experiment)
 app <- init(
   data = data,
@@ -175,17 +206,19 @@ 
    Examples
    + +
    + + - - + + diff --git a/v0.1.6/reference/top_gene_plot.html b/v0.1.6/reference/top_gene_plot.html index 4897a425..990084a9 100644 --- a/v0.1.6/reference/top_gene_plot.html +++ b/v0.1.6/reference/top_gene_plot.html @@ -1,10 +1,26 @@ - -Most Expressed Genes Plot — top_gene_plot • teal.modules.hermes + + + + + + + + Skip to contents @@ -20,7 +36,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -66,46 +88,54 @@
    -

    Usage

    +

    Usage +

    top_gene_plot(object, assay_name)
    -

    Arguments

    -
    object
    +

    Arguments +

    +
    +
    object

    (AnyHermesData)
    contains RNA-seq values for one experiment.

    assay_name

    (string)
    the assay to define the groups.

    -
    + +
    -

    Value

    +

    Value +

    Plot to be displayed in the teal app.

    -

    Examples

    +

    Examples +

    library(hermes)
 object <- HermesData(summarized_experiment)
 result <- top_gene_plot(object, assay_name = "counts")
    + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/reference/validate_gene_spec.html b/v0.1.6/reference/validate_gene_spec.html index 4dabc496..031b536f 100644 --- a/v0.1.6/reference/validate_gene_spec.html +++ b/v0.1.6/reference/validate_gene_spec.html @@ -1,12 +1,28 @@ - - + + + + + +Validation of Gene Specification — validate_gene_spec • teal.modules.hermes +Validation of Gene Specification — validate_gene_spec • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,33 +91,39 @@
    -

    Usage

    +

    Usage +

    validate_gene_spec(gene_spec, gene_choices)
    -

    Arguments

    -
    gene_spec
    +

    Arguments +

    +
    +
    gene_spec

    (GeneSpec)
    gene specification.

    gene_choices

    (character)
    all possible gene choices.

    -
    + + + +

    teal.modules.hermes is a part of the NEST and pharmaverse.

    -
    + + - - + + diff --git a/v0.1.6/reference/validate_n_levels.html b/v0.1.6/reference/validate_n_levels.html index 7fa7be99..3922838b 100644 --- a/v0.1.6/reference/validate_n_levels.html +++ b/v0.1.6/reference/validate_n_levels.html @@ -1,12 +1,28 @@ - - + + + + + +Validation of Number of Levels — validate_n_levels • teal.modules.hermes +Validation of Number of Levels — validate_n_levels • teal.modules.hermes + + + + + + + + + + Skip to contents @@ -22,7 +38,8 @@ + - + + -
    • +
        +
        • -
      +
    + @@ -69,13 +91,16 @@
    -

    Usage

    +

    Usage +

    validate_n_levels(x, name, n_levels)
    -

    Arguments

    -
    x
    +

    Arguments +

    +
    +
    x

    (factor)
    factor to validate.

    @@ -86,20 +111,23 @@

    Arguments

    + + + + - - + +