update readmes and description (#464)

Related to insightsengineering/coredev-tasks#462 --------- Signed-off-by: Marcin <[email protected]> Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com> Co-authored-by: Dony Unardi
insightsengineering · Sep 19, 2023 · 3dfcb18 · 3dfcb18
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,3 +1,5 @@
+LICENSE
+^assets$
 ^renv$
 ^renv\.lock$
 CODE_OF_CONDUCT.md

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -94,17 +94,17 @@ This repository follows the standard [`tidyverse` style guide](https://style.tid
 
 ### Dependency management
 
-Lightweight is the right weight. This repository follows [tinyverse](https://www.tinyverse.org/) recommedations of limiting dependencies to minimum.
+Lightweight is the right weight. This repository follows [tinyverse](https://www.tinyverse.org/) recommendations of limiting dependencies to minimum.
 
 ### 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)`.
+If the code is not compatible with all (!) historical versions of a given dependency 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
 
 #### 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()`.
+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.
 
@@ -130,7 +130,7 @@ The package maintainer also reserves the right to adjust the criteria to recogni
 If you have further questions regarding the contribution guidelines, please contact the package/repository maintainer.
 
 <!-- urls -->
-[docs]: https://insightsengineering.github.io/teal.slice/index.html
-[articles]: https://insightsengineering.github.io/teal.slice/main/articles/index.html
-[license]: https://insightsengineering.github.io/teal.slice/main/LICENSE-text.html
+[docs]: https://insightsengineering.github.io/teal.slice/latest-tag/index.html
+[articles]: https://insightsengineering.github.io/teal.slice/latest-tag/articles/index.html
+[license]: https://insightsengineering.github.io/teal.slice/latest-tag/LICENSE-text.html
 [insights]: https://github.com/insightsengineering/teal.slice/pulse
diff --git a/.github/ISSUE_TEMPLATE/bug.yml b/.github/ISSUE_TEMPLATE/bug.yml
@@ -33,15 +33,15 @@ body:
     id: code-of-conduct
     attributes:
       label: Code of Conduct
-      description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal.slice/CODE_OF_CONDUCT.html)
+      description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal.slice/latest-tag/CODE_OF_CONDUCT.html)
       options:
         - label: I agree to follow this project's Code of Conduct.
           required: true
   - type: checkboxes
     id: contributor-guidelines
     attributes:
       label: Contribution Guidelines
-      description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal.slice/CONTRIBUTING.html)
+      description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal.slice/latest-tag/CONTRIBUTING.html)
       options:
         - label: I agree to follow this project's Contribution Guidelines.
           required: true

diff --git a/.github/ISSUE_TEMPLATE/feature.yml b/.github/ISSUE_TEMPLATE/feature.yml
@@ -13,15 +13,15 @@ body:
     id: code-of-conduct
     attributes:
       label: Code of Conduct
-      description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal.slice/CODE_OF_CONDUCT.html)
+      description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal.slice/latest-tag/CODE_OF_CONDUCT.html)
       options:
         - label: I agree to follow this project's Code of Conduct.
           required: true
   - type: checkboxes
     id: contributor-guidelines
     attributes:
       label: Contribution Guidelines
-      description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal.slice/CONTRIBUTING.html)
+      description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal.slice/latest-tag/CONTRIBUTING.html)
       options:
         - label: I agree to follow this project's Contribution Guidelines.
           required: true

diff --git a/.github/ISSUE_TEMPLATE/question.yml b/.github/ISSUE_TEMPLATE/question.yml
@@ -13,15 +13,15 @@ body:
     id: code-of-conduct
     attributes:
       label: Code of Conduct
-      description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal.slice/CODE_OF_CONDUCT.html)
+      description: By submitting this issue, you agree to follow our [Code of Conduct.](https://insightsengineering.github.io/teal.slice/latest-tag/CODE_OF_CONDUCT.html)
       options:
         - label: I agree to follow this project's Code of Conduct.
           required: true
   - type: checkboxes
     id: contributor-guidelines
     attributes:
       label: Contribution Guidelines
-      description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal.slice/CONTRIBUTING.html)
+      description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://insightsengineering.github.io/teal.slice/latest-tag/CONTRIBUTING.html)
       options:
         - label: I agree to follow this project's Contribution Guidelines.
           required: true

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Type: Package
 Package: teal.slice
-Title: Filter Module for `teal` Applications
+Title: Filter Module for 'teal' Applications
 Version: 0.4.0.9012
 Date: 2023-09-08
 Authors@R: c(
@@ -19,8 +19,13 @@ Authors@R: c(
     person("Junlue", "Zhao", role = "aut"),
     person("F. Hoffmann-La Roche AG", role = c("cph", "fnd"))
   )
-Description: Filter module for teal applications.
-License: Apache License 2.0 | file LICENSE
+Description: 
+    Module containing filter panel for 'teal' applications. Allows for interactive filtering of data stored in 
+    'data.frame' and 'MultiAssayExperiment' objects. Also displays filtered and unfiltered observation counts.
+License: Apache License 2.0
+URL: https://insightsengineering.github.io/teal.slice/,
+    https://github.com/insightsengineering/teal.slice/
+BugReports: https://github.com/insightsengineering/teal.slice/issues
 Depends:
     R (>= 4.0),
     shiny

diff --git a/README.md b/README.md
@@ -27,17 +27,33 @@
 
 ## Installation
 
-From July 2023 `insightsengineering` packages are available on [r-universe](https://r-universe.dev/).
-
 ```r
 # stable versions
-install.packages('teal.slice', repos = c('https://insightsengineering.r-universe.dev', 'https://cloud.r-project.org'))
+install.packages('teal.slice', repos = c('https://insightsengineering.r-universe.dev', getOption('repos')))
+
+# install.packages("pak")
+pak::pak("insightsengineering/teal.slice@*release")
+```
 
+Alternatively, you might want to use the development version available on [r-universe](https://r-universe.dev/).
+
+```r
 # beta versions
-install.packages('teal.slice', repos = c('https://pharmaverse.r-universe.dev', 'https://cloud.r-project.org'))
+install.packages('teal.slice', repos = c('https://pharmaverse.r-universe.dev', getOption('repos')))
+
+# install.packages("pak")
+pak::pak("insightsengineering/teal.slice")
 ```
 
-See package vignettes `browseVignettes(package = "teal.slice")` for usage of this package.
+## Usage
+
+To understand how to use this package, please refer to the [Introduction to teal.slice](https://insightsengineering.github.io/teal.slice/latest-tag/articles/teal-slice.html) article, which provides multiple examples of code implementation.
+
+![Showcase](https://github.com/insightsengineering/teal.slice/blob/main/assets/img/showcase.gif)
+
+## Getting help
+
+If you encounter a bug or you have a feature request - please file an issue. For questions, discussions and staying up to date, please use the "teal" channel in the [`pharmaverse` slack workspace](https://pharmaverse.slack.com).
 
 ## Stargazers and Forkers
 

diff --git a/assets/img/showcase.gif b/assets/img/showcase.gif
diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -1,10 +1,21 @@
-Forkers
-Hoffmann
-UI
 cloneable
+Forkers
 funder
+github
+Hoffmann
+https
+insightsengineering
+io
+Pre
 programmatically
 repo
 reproducibility
+sessionInfo
 subclasses
 subtype
+textarea
+tinyverse
+UI
+upvote
+sessionInfo
+MultiAssayExperiment
diff --git a/man/teal.slice-package.Rd b/man/teal.slice-package.Rd
diff --git a/vignettes/filter-panel-for-developers.Rmd b/vignettes/filter-panel-for-developers.Rmd
@@ -1,10 +1,9 @@
 ---
-title: "Filter panel for developers"
-author: "NEST Core Dev Team"
-date: "10/07/2023"
+title: "Filter Panel for Developers"
+author: "NEST CoreDev"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Filter panel for developers}
+  %\VignetteIndexEntry{Filter Panel for Developers}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -21,13 +20,13 @@ These methods include:
 - `remove_filter_state` - removes particular filter states based on `teal_slices` object
 - `clear_filter_states` - removes all filter states
 
-Setting and getting filter states are done through `teal_slices` object which is a collection of `teal_slice` objects. 
+Setting and getting filter states are done through `teal_slices` object which is a collection of `teal_slice` objects.
 Think of a `teal_slice` as a quantum of information that fully describes the filter state of one variable.
 
-In order to tell `FilteredData` to set a filter for a specific variable, 
-one must call the `set_filter_state` method with a `teal_slices` object containing a `teal_slice` 
+In order to tell `FilteredData` to set a filter for a specific variable,
+one must call the `set_filter_state` method with a `teal_slices` object containing a `teal_slice`
 that refers to the variable of interest.
-To remove a particular `FilterState` object, one must call the `remove_filter_state` method 
+To remove a particular `FilterState` object, one must call the `remove_filter_state` method
 using a `teal_slices` containing a `teal_slice` that refers to the respective variable.
 
 Each `teal_slice` object contains all the information necessary to:
@@ -37,7 +36,7 @@ Each `teal_slice` object contains all the information necessary to:
    - `dataname` - name of the data set
    - `varname` - name of the column
    - `experiment` (only for `MultiAssayExperiment` objects) - name of the experiment
-   - `arg` (only for `SummarizedExperiment` objects, e.g within a `MultiAssayExperiment`) - 
+   - `arg` (only for `SummarizedExperiment` objects, e.g within a `MultiAssayExperiment`) -
    name of the argument in the call to `subset` (`subset` of `select`)
 
 2. Express or store the current selection state:
@@ -50,16 +49,16 @@ Each `teal_slice` object contains all the information necessary to:
 3. Control the behavior and appearance of the `FilterState` object:
 
    - `choices` - determines the set of values or the range that can be selected from
-   - `multiple` (only for `ChoiceFilterState`) - allows multiple values to be selected 
+   - `multiple` (only for `ChoiceFilterState`) - allows multiple values to be selected
    - `fixed` - forbids changing state of the `FilterState`
    - `anchored` - forbids removal of the `FilterState`
    - `title` - displayed title of the filter card
 
-In addition, every `teal_slice` object has an `id`. 
+In addition, every `teal_slice` object has an `id`.
 
 It is impossible to create `FilteredData` with slices with duplicated `id`s.
 This is because filter states are both created and modified with the `set_filter_state` method
-so if two consecutive calls to `set_filter_state` are passed a `teal_slice` with the same id, 
+so if two consecutive calls to `set_filter_state` are passed a `teal_slice` with the same id,
 the first call will instantiate a `FilterState`, and the second call will modify it.
 
 Creating `teal_slices` with slices with duplicated `id`s is forbidden and will raise an error.
@@ -120,12 +119,12 @@ clear_filter_states(datasets)
 
 ### Controlling settings of the filter panel
 
-In addition to controlling individual filter states through `set_filter_state`, 
-one can also manage some general behaviors of the whole filter panel. 
+In addition to controlling individual filter states through `set_filter_state`,
+one can also manage some general behaviors of the whole filter panel.
 This can be done with arguments of the `teal_slices` function:
 
-1. `include_varnames` defines which columns in the used data sets are allowed to be filtered on. 
-In the following example only two columns of `iris` and two columns of `mtcars` will be able to have filters set. 
+1. `include_varnames` defines which columns in the used data sets are allowed to be filtered on.
+In the following example only two columns of `iris` and two columns of `mtcars` will be able to have filters set.
 ```{r}
 set_filter_state(
   datasets,
@@ -159,7 +158,7 @@ set_filter_state(
 | Distribution in unfiltered data | Filtered vs. unfiltered distribution  |
 | ![](./images/filter_panel/count_type_none.jpeg){width=300} | ![](./images/filter_panel/count_type_all.jpeg){width=300} |
 
-4. `allow_add` determines whether the "Add Filter Variables" module will be displayed 
+4. `allow_add` determines whether the "Add Filter Variables" module will be displayed
 to allow the user to add new filters.