Merge branch 'main' into propagation-march-2024

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.0
+    rev: v0.4.1
     hooks:
       - id: style-files
         name: Style code with `styler`
@@ -24,7 +24,6 @@ repos:
           - forcats
           - bioc::hermes
           - lifecycle
-          - logger
           - bioc::MultiAssayExperiment
           - rtables
           - S4Vectors

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.modules.hermes
 Title: RNA-Seq Analysis Modules to Add to a Teal Application
-Version: 0.1.6.9003
-Date: 2024-02-22
+Version: 0.1.6.9010
+Date: 2024-04-02
 Authors@R: c(
     person("Daniel", "Sabanés Bové", , "[email protected]", role = c("aut", "cre")),
     person("Nikolas", "Burkoff", role = "aut"),
@@ -40,7 +40,6 @@ Imports:
     forcats,
     hermes (>= 1.7.1),
     lifecycle,
-    logger (>= 0.2.0),
     MultiAssayExperiment,
     rtables (>= 0.5.1),
     S4Vectors,
@@ -50,16 +49,18 @@ Imports:
     stringr,
     SummarizedExperiment,
     teal.data (>= 0.3.0.9018),
-    teal.logger (>= 0.1.1),
+    teal.logger (>= 0.1.3.9013),
     teal.reporter (>= 0.2.0),
     teal.widgets (>= 0.4.0),
-    tern (>= 0.7.10)
+    tern (>= 0.7.10),
+    utils
 Suggests:
     BiocStyle,
     covr,
     dplyr,
     globals,
     knitr,
+    logger (>= 0.2.0),
     matrixStats,
     R6,
     rmarkdown,

NAMESPACE

@@ -73,3 +73,4 @@ import(teal.data)
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,setListElement)
 importFrom(lifecycle,deprecate_soft)
+importFrom(utils,str)

NEWS.md

@@ -1,4 +1,4 @@
-# teal.modules.hermes 0.1.6.9003
+# teal.modules.hermes 0.1.6.9010
 
 ### Miscellaneous
 * Added placeholders for `assaySpec`, `adtteSpec` and `geneSpec` inputs when no option is selected.

R/adtteSpec.R

@@ -162,7 +162,7 @@ adtteSpecInput <- function(inputId, # nolint
 #'   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 #'   moduleServer(id, function(input, output, session) {
 #'     output$encoding_ui <- renderUI({
-#'       div(
+#'       tags$div(
 #'         experimentSpecInput(session$ns("experiment"), data, mae_name = "MAE"),
 #'         assaySpecInput(session$ns("assay")),
 #'         geneSpecInput(session$ns("genes"), funs = list(Mean = colMeans)),

R/argument_convention.R

@@ -43,6 +43,7 @@
 #' @param plot_width (`list`)\cr list of integers to set the default, minimum,
 #'   and maximum plot width.
 #' @param filter_panel_api (`FilterPanelAPI`)\cr object describing the actual filter panel API.
+#' @param .test (`flag`)\cr whether to display the internal structure of the plot for testing purposes.
 #'
 #' @name module_arguments
 #' @keywords internal

R/assaySpec.R

@@ -55,7 +55,7 @@ assaySpecInput <- function(inputId, # nolint
 #' server <- function(id, data, filter_panel_api) {
 #'   moduleServer(id, module = function(input, output, session) {
 #'     output$encoding_ui <- renderUI({
-#'       div(
+#'       tags$div(
 #'         experimentSpecInput(session$ns("experiment"), data, "MAE"),
 #'         assaySpecInput(
 #'           session$ns("assay"),

R/barplot.R

@@ -34,29 +34,33 @@ tm_g_barplot <- function(label,
                            Max = matrixStats::colMaxs
                          ),
                          pre_output = NULL,
-                         post_output = NULL) {
-  logger::log_info("Initializing tm_g_barplot")
+                         post_output = NULL,
+                         .test = FALSE) {
+  message("Initializing tm_g_barplot")
   assert_string(label)
   assert_string(mae_name)
   assert_character(exclude_assays)
   assert_summary_funs(summary_funs)
   assert_tag(pre_output, null.ok = TRUE)
   assert_tag(post_output, null.ok = TRUE)
+  assert_flag(.test)
 
   module(
     label = label,
     server = srv_g_barplot,
     server_args = list(
       mae_name = mae_name,
       exclude_assays = exclude_assays,
-      summary_funs = summary_funs
+      summary_funs = summary_funs,
+      .test = .test
     ),
     ui = ui_g_barplot,
     ui_args = list(
       mae_name = mae_name,
       summary_funs = summary_funs,
       pre_output = pre_output,
-      post_output = post_output
+      post_output = post_output,
+      .test = .test
     ),
     datanames = mae_name
   )
@@ -69,10 +73,11 @@ ui_g_barplot <- function(id,
                          mae_name,
                          summary_funs,
                          pre_output,
-                         post_output) {
+                         post_output,
+                         .test = FALSE) {
   ns <- NS(id)
   teal.widgets::standard_layout(
-    encoding = div(
+    encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###
@@ -101,7 +106,10 @@ ui_g_barplot <- function(id,
         )
       )
     ),
-    output = teal.widgets::plot_with_settings_ui(ns("plot")),
+    output = div(
+      if (.test) verbatimTextOutput(ns("table")) else NULL,
+      teal.widgets::plot_with_settings_ui(ns("plot"))
+    ),
     pre_output = pre_output,
     post_output = post_output
   )
@@ -116,11 +124,13 @@ srv_g_barplot <- function(id,
                           reporter,
                           mae_name,
                           exclude_assays,
-                          summary_funs) {
+                          summary_funs,
+                          .test = FALSE) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   assert_class(filter_panel_api, "FilterPanelAPI")
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
+  assert_flag(.test)
   moduleServer(id, function(input, output, session) {
     output$experiment_ui <- renderUI({
       experimentSpecInput(session$ns("experiment"), data, mae_name)
@@ -189,6 +199,13 @@ srv_g_barplot <- function(id,
       plot_r = plot_r
     )
 
+    if (.test) {
+      table_r <- reactive({
+        utils::str(layer_data(plot_r()))
+      })
+      output$table <- renderPrint(table_r())
+    }
+
     ### REPORTER
     if (with_reporter) {
       card_fun <- function(comment, label) {
@@ -230,6 +247,7 @@ srv_g_barplot <- function(id,
           card$append_text("Comment", "header3")
           card$append_text(comment)
         }
+
         card
       }
       teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)
@@ -246,14 +264,15 @@ srv_g_barplot <- function(id,
 #' if (interactive()) {
 #'   sample_tm_g_barplot()
 #' }
-sample_tm_g_barplot <- function() {
+sample_tm_g_barplot <- function(.test = FALSE) {
   data <- teal.data::teal_data(MAE = hermes::multi_assay_experiment)
   app <- teal::init(
     data = data,
     modules = teal::modules(
       tm_g_barplot(
         label = "barplot",
-        mae_name = "MAE"
+        mae_name = "MAE",
+        .test = .test
       )
     )
   )

R/boxplot.R

@@ -35,29 +35,33 @@ tm_g_boxplot <- function(label,
                            Max = matrixStats::colMaxs
                          ),
                          pre_output = NULL,
-                         post_output = NULL) {
-  logger::log_info("Initializing tm_g_boxplot")
+                         post_output = NULL,
+                         .test = FALSE) {
+  message("Initializing tm_g_boxplot")
   assert_string(label)
   assert_string(mae_name)
   assert_character(exclude_assays, any.missing = FALSE)
   assert_summary_funs(summary_funs, null.ok = TRUE)
   assert_tag(pre_output, null.ok = TRUE)
   assert_tag(post_output, null.ok = TRUE)
+  assert_flag(.test)
 
   teal::module(
     label = label,
     server = srv_g_boxplot,
     server_args = list(
       mae_name = mae_name,
       summary_funs = summary_funs,
-      exclude_assays = exclude_assays
+      exclude_assays = exclude_assays,
+      .test = .test
     ),
     ui = ui_g_boxplot,
     ui_args = list(
       mae_name = mae_name,
       summary_funs = summary_funs,
       pre_output = pre_output,
-      post_output = post_output
+      post_output = post_output,
+      .test = .test
     ),
     datanames = mae_name
   )
@@ -70,10 +74,11 @@ ui_g_boxplot <- function(id,
                          mae_name,
                          summary_funs,
                          pre_output,
-                         post_output) {
+                         post_output,
+                         .test = FALSE) {
   ns <- NS(id)
   teal.widgets::standard_layout(
-    encoding = div(
+    encoding = tags$div(
       ### Reporter
       teal.reporter::simple_reporter_ui(ns("simple_reporter")),
       ###
@@ -97,7 +102,10 @@ ui_g_boxplot <- function(id,
         )
       )
     ),
-    output = teal.widgets::plot_with_settings_ui(ns("plot")),
+    output = div(
+      if (.test) verbatimTextOutput(ns("table")) else NULL,
+      teal.widgets::plot_with_settings_ui(ns("plot"))
+    ),
     pre_output = pre_output,
     post_output = post_output
   )
@@ -112,7 +120,8 @@ srv_g_boxplot <- function(id,
                           reporter,
                           mae_name,
                           exclude_assays,
-                          summary_funs) {
+                          summary_funs,
+                          .test = FALSE) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   assert_class(filter_panel_api, "FilterPanelAPI")
   checkmate::assert_class(data, "reactive")
@@ -184,6 +193,13 @@ srv_g_boxplot <- function(id,
       plot_r = plot_r
     )
 
+    if (.test) {
+      table_r <- reactive({
+        utils::str(layer_data(plot_r()))
+      })
+      output$table <- renderPrint(table_r())
+    }
+
     ### REPORTER
     if (with_reporter) {
       card_fun <- function(comment, label) {
@@ -247,14 +263,15 @@ srv_g_boxplot <- function(id,
 #' if (interactive()) {
 #'   sample_tm_g_boxplot()
 #' }
-sample_tm_g_boxplot <- function() {
+sample_tm_g_boxplot <- function(.test = FALSE) {
   data <- teal.data::teal_data(MAE = hermes::multi_assay_experiment)
   app <- teal::init(
     data = data,
     modules = teal::modules(
       tm_g_boxplot(
         label = "boxplot",
-        mae_name = "MAE"
+        mae_name = "MAE",
+        .test = .test
       )
     )
   )

R/experimentSpec.R

@@ -132,7 +132,7 @@ h_gene_data <- function(object, name_annotation) {
 #'   ns <- NS(id)
 #'   teal.widgets::standard_layout(
 #'     encoding = uiOutput(ns("encoding_ui")),
-#'     output = div(
+#'     output = tags$div(
 #'       verbatimTextOutput(ns("summary")),
 #'       verbatimTextOutput(ns("head"))
 #'     )
@@ -145,7 +145,7 @@ h_gene_data <- function(object, name_annotation) {
 #'                    mae_name) {
 #'   moduleServer(id, function(input, output, session) {
 #'     output$encoding_ui <- renderUI({
-#'       div(
+#'       tags$div(
 #'         experimentSpecInput(
 #'           session$ns("my_experiment"),
 #'           data,