Merge branch 'main' into 239_log_shiny_input_change@main

Signed-off-by: Marcin <[email protected]>

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.modules.hermes
 Title: RNA-Seq Analysis Modules to Add to a Teal Application
-Version: 0.1.6.9013
-Date: 2024-04-30
+Version: 0.1.6.9014
+Date: 2024-05-13
 Authors@R: c(
     person("Daniel", "Sabanés Bové", , "[email protected]", role = c("aut", "cre")),
     person("Nikolas", "Burkoff", role = "aut"),
@@ -29,26 +29,26 @@ URL: https://insightsengineering.github.io/teal.modules.hermes/,
 BugReports: 
     https://github.com/insightsengineering/teal.modules.hermes/issues
 Depends:
-    R (>= 4.1),
     ggplot2,
+    R (>= 4.1),
     shiny,
     teal (>= 0.15.0)
 Imports:
-    DT,
-    MultiAssayExperiment,
-    S4Vectors,
-    SummarizedExperiment,
     checkmate,
+    DT,
     edgeR,
     forcats,
     hermes (>= 1.7.1),
     lifecycle,
     logger (>= 0.3.0),
+    MultiAssayExperiment,
     rtables (>= 0.5.1),
+    S4Vectors,
     shinyRadioMatrix (>= 0.2.1),
     shinyWidgets,
     stats,
     stringr,
+    SummarizedExperiment,
     teal.data (>= 0.3.0.9018),
     teal.logger (>= 0.1.3.9013),
     teal.reporter (>= 0.2.0),
@@ -57,12 +57,12 @@ Imports:
     utils
 Suggests:
     BiocStyle,
-    R6,
     covr,
     dplyr,
     globals,
     knitr,
     matrixStats,
+    R6,
     rmarkdown,
     rvest,
     shinytest2 (>= 0.2.0),
@@ -71,11 +71,11 @@ VignetteBuilder:
     knitr
 RdMacros:
     lifecycle
+biocViews:
 Config/Needs/website: insightsengineering/nesttemplate
 Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
-biocViews:

NEWS.md

@@ -1,4 +1,4 @@
-# teal.modules.hermes 0.1.6.9013
+# teal.modules.hermes 0.1.6.9014
 
 ### Miscellaneous
 * Added placeholders for `assaySpec`, `adtteSpec` and `geneSpec` inputs when no option is selected.

inst/WORDLIST

@@ -1,10 +1,8 @@
-Bové
 Forkers
 Hoffmann
 Lyndsee
 Midori
 RNAseq
-Sabanés
 UI
 funder
 hermes

tests/testthat/test-pca.R

@@ -62,18 +62,19 @@ test_that("pca module works as expected in the test app", {
   )
 
   # Add a gene filter and deselect everything and check that it does not crash.
-  app$set_inputs(!!ns2("add-MAE-hd1-row_to_add") := "symbol")
+  app$set_inputs(!!ns2("add-MAE-hd1-row_to_add") := "chromosome_name")
   app$wait_for_idle()
-  app$set_inputs(!!ns2("active-MAE-hd1-MAE_symbol_hd1_subset-inputs-selection_open") := TRUE, allow_no_input_binding_ = TRUE)
-  app$set_inputs(!!ns2("active-MAE-hd1-MAE_symbol_hd1_subset-inputs-selection") := character())
-  app$set_inputs(!!ns2("active-MAE-hd1-MAE_symbol_hd1_subset-inputs-selection_open") := FALSE, allow_no_input_binding_ = TRUE)
+  app$set_inputs(!!ns2("active-MAE-hd1-MAE_chromosome_name_hd1_subset-inputs-selection_open") := TRUE, allow_no_input_binding_ = TRUE)
+  app$set_inputs(!!ns2("active-MAE-hd1-MAE_chromosome_name_hd1_subset-inputs-keep_na-value") := FALSE)
+  app$set_inputs(!!ns2("active-MAE-hd1-MAE_chromosome_name_hd1_subset-inputs-selection") := character())
+  app$set_inputs(!!ns2("active-MAE-hd1-MAE_chromosome_name_hd1_subset-inputs-selection_open") := FALSE, allow_no_input_binding_ = TRUE)
 
   app$wait_for_idle()
   res <- app$get_value(output = ns("test_pca"))
   expect_match(res$message, "No genes or samples included in this experiment, please adjust filters")
 
   # Remove filters
-  app$click(ns2("active-MAE-hd1-MAE_symbol_hd1_subset-remove"))
+  app$click(ns2("active-MAE-hd1-MAE_chromosome_name_hd1_subset-remove"))
 
   # Update the tab selection.
   app$set_inputs(!!ns("tab_selected") := "PC and Sample Correlation")