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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 0.1.6.9022, 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 0.1.6.9022, 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\") #>
    #>
    #>