feat: upload tranlation and defaults for proteomics

bigomics · Jul 16, 2024 · 438b628 · 438b628
1 parent 8a8e3f7
commit 438b628
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Showing 6 changed files with 32 additions and 11 deletions.
diff --git a/components/app/R/server.R b/components/app/R/server.R
@@ -211,7 +211,7 @@ app_server <- function(input, output, session) {
 
   ## Modules needed from the start
   if (opt$ENABLE_UPLOAD) {
-    UploadBoard(
+    upload_datatype <-UploadBoard(
       id = "upload",
       pgx_dir = PGX.DIR,
       pgx = PGX,
@@ -225,6 +225,12 @@ app_server <- function(input, output, session) {
     )
   }
 
+  shiny::observeEvent(upload_datatype(), {
+    if (tolower(upload_datatype()) == "proteomics") {
+      shiny.i18n::update_lang("proteomics", session)
+    }
+  })
+
 
   ## Modules needed after dataset is loaded (deferred) --------------
   observeEvent(env$load$is_data_loaded(), {

diff --git a/components/board.upload/R/upload_module_computepgx.R b/components/board.upload/R/upload_module_computepgx.R
@@ -39,10 +39,20 @@ upload_module_computepgx_server <- function(
     function(input, output, session) {
       ns <- session$ns
       ## statistical method for GENE level testing
-      GENETEST.METHODS <- c(
-        "ttest", "ttest.welch", "voom.limma", "trend.limma", "notrend.limma",
-        "deseq2.wald", "deseq2.lrt", "edger.qlf", "edger.lrt"
-      )
+      GENETEST.METHODS <- shiny::reactiveVal("")
+      shiny::observeEvent(upload_datatype(), {
+        if (tolower(upload_datatype()) == "proteomics") {
+          GENETEST.METHODS(
+            c("ttest", "ttest.welch", "trend.limma", "notrend.limma")
+          )
+        } else {
+          GENETEST.METHODS(
+            c("ttest", "ttest.welch", "voom.limma", "trend.limma", "notrend.limma",
+            "deseq2.wald", "deseq2.lrt", "edger.qlf", "edger.lrt")
+          )
+        }
+      })
+
       ## GENETEST.SELECTED <- c("trend.limma", "voom.limma", "deseq2.wald", "edger.qlf")
       GENETEST.SELECTED <- c("ttest", "ttest.welch", "trend.limma", "notrend.limma") 
 
@@ -148,7 +158,7 @@ upload_module_computepgx_server <- function(
                 shiny::checkboxGroupInput(
                   ns("gene_methods"),
                   shiny::HTML("<h4>Gene tests:</h4>"),
-                  GENETEST.METHODS,
+                  GENETEST.METHODS(),
                   selected = GENETEST.SELECTED
                 )
               ),

diff --git a/components/board.upload/R/upload_module_outliers.R b/components/board.upload/R/upload_module_outliers.R
@@ -682,12 +682,12 @@ upload_module_outliers_server <- function(
                   div("Normalize data values:\n"),
                   shiny::selectInput(ns("scaling_method"), NULL,
                     choices = c(
-                      "LogCPM (default)" = "CPM", ## log2(nC+1)
+                      "LogCPM" = "CPM", ## log2(nC+1)
                       "LogMaxMedian" = "logMaxMedian",
                       "LogMaxSum" = "logMaxSum",
                       "Skip normalization" = "Skip_normalization"
                     ),
-                    selected = "CPM"
+                    selected = ifelse(tolower(upload_datatype()) == "proteomics", "logMaxMedian", "CPM")
                   ),
                   shiny::checkboxInput(ns("quantile_norm"), "Quantile normalization", value = TRUE),
                   br()

diff --git a/components/board.upload/R/upload_server.R b/components/board.upload/R/upload_server.R
@@ -12,7 +12,7 @@ UploadBoard <- function(id,
                         recompute_pgx,
                         recompute_info,
                         inactivityCounter,
-                        new_upload) {
+                        new_upload, session2) {
   moduleServer(id, function(input, output, session) {
     ns <- session$ns ## NAMESPACE
 
@@ -839,7 +839,7 @@ UploadBoard <- function(id,
       scrollY = "calc(50vh - 140px)",
       width = c("auto", "100%"),
       height = c("100%", TABLE_HEIGHT_MODAL),
-      title = "Uploaded Counts",
+      title = ifelse(tolower(upload_datatype()) == "proteomics", "Uploaded Expression", "Uploaded Counts"),
       info.text = "This is the uploaded counts data.",
       caption = "This is the uploaded counts data."
     )
@@ -941,5 +941,6 @@ UploadBoard <- function(id,
     ## ------------------------------------------------
     ## Board return object
     ## ------------------------------------------------
+    return(upload_datatype)
   })
 }
diff --git a/components/board.upload/R/upload_ui.R b/components/board.upload/R/upload_ui.R
@@ -19,7 +19,7 @@ UploadUI <- function(id) {
   )
 
   counts_ui <- wizardR::wizard_step(
-    step_title = "Step 2: Upload counts",
+    step_title = tspan("Step 2: Upload counts"),
     step_id = "step_counts",
     upload_table_preview_counts_ui(
       ns("counts_preview")

diff --git a/etc/translation.json b/etc/translation.json
@@ -65,6 +65,10 @@
         {
             "RNA-seq": "Counts boxplots",
             "proteomics": "Abundance boxplots"
+        },
+        {
+            "RNA-seq": "Step 2: Upload counts",
+            "proteomics": "Step 2: Upload expression"
         }
       ]
   }