[FEAT] - backbone of a log transform step

Author: leopoldguyot

R/interface_module_log_transform_tab.R

@@ -0,0 +1,46 @@
+#' log transform tab (section) ui builder
+#'
+#' @return A shiny tagList object that contains the log transform tab UI components
+#' @rdname INTERNAL_interface_module_log_transform_tab
+#' @keywords internal
+#'
+#' @importFrom shiny fluidRow NS actionButton icon uiOutput
+#' @importFrom shinydashboardPlus box
+#' @importFrom htmltools tagList
+#' @importFrom shinyBS bsTooltip
+#'
+interface_module_log_transform_tab <- function(id) {
+    tagList(
+        actionButton(
+            NS(id, "reload"),
+            "Load assays from previous step",
+            icon("hand-pointer", class = "fa-solid"),
+            width = "100%",
+            class = "load-button"
+        ),
+        shinyBS::bsTooltip(
+            id = NS(id, "reload"),
+            title = paste("Load the assays from the previous step.",
+                "Click on this button the first time you visit this page",
+                "or if you updated the assays from the previous steps.",
+                sep = " "
+            ),
+            trigger = "hover"
+        ),
+    )
+}
+
+interface_box_distribution <- function(id) {
+    box(
+        title = "Log Transformation",
+        status = "primary",
+        width = 12,
+        solidHeader = TRUE,
+        collapsible = FALSE,
+        
+        withSpinner(plotlyOutput(outputId = NS(id, "dist")),
+            type = 6,
+            color = "#3c8dbc"
+        )
+    )
+}

R/server_dynamic_workflow.R

@@ -34,13 +34,17 @@ server_dynamic_workflow <- function(input, output, session) {
             dynamic_tabs <- lapply(seq_along(global_rv$workflow_config), function(i) {
                 tabItem(
                     tabName = paste0("step_", i),
-                    if (global_rv$workflow_config[[i]] == "Cells Filtering") {
+                    if (global_rv$workflow_config[[i]] == "Samples Filtering") {
                         interface_module_samples_filtering_tab(
-                            paste0("filtering_", i)
+                            paste0("samples_filtering_", i)
                         )
-                    } else {
+                    } else if(global_rv$workflow_config[[i]] == "Features Filtering") {
                         interface_module_features_filtering_tab(
-                            paste0("filtering_", i)
+                            paste0("features_filtering_", i)
+                        )
+                    } else if(global_rv$workflow_config[[i]] == "Log Transformation") {
+                        interface_module_log_transform_tab(
+                            paste0("log_transform_", i)
                         )
                     }
                 )
@@ -50,12 +54,16 @@ server_dynamic_workflow <- function(input, output, session) {
         })
 
         lapply(seq_along(global_rv$workflow_config), function(i) {
-            if (global_rv$workflow_config[[i]] == "Cells Filtering") {
-                server_module_samples_filtering_tab(paste0("filtering_", i),
+            if (global_rv$workflow_config[[i]] == "Samples Filtering") {
+                server_module_samples_filtering_tab(paste0("samples_filtering_", i),
+                    step_number = i
+                )
+            } else if(global_rv$workflow_config[[i]] == "Features Filtering") {
+                server_module_features_filtering_tab(paste0("features_filtering_", i),
                     step_number = i
                 )
-            } else {
-                server_module_features_filtering_tab(paste0("filtering_", i),
+            } else if(global_rv$workflow_config[[i]] == "Log Transformation") {
+                server_module_log_transform_tab(paste0("log_transform_", i),
                     step_number = i
                 )
             }

R/server_module_log_transform_tab.R

@@ -0,0 +1,15 @@
+#' Server for the module log transformation tab
+#'
+#' @param id module id
+#' @return The server logic for the log transformation tab
+#' @rdname INTERNAL_server_module_log_transformation_tab
+#' @keywords internal
+#'
+#' @importFrom shiny moduleServer updateSelectInput observeEvent eventReactive is.reactive
+#' @importFrom MultiAssayExperiment getWithColData
+#'
+server_module_log_transform_tab <- function(id, step_number) {
+    moduleServer(id, function(input, output, session) {
+        return(NULL)
+    })
+    }

R/server_module_qc_metrics.R

@@ -1,4 +1,4 @@
-#' Title
+#' Server module for qc metrics box
 #'
 #' @param id module id
 #' @param assays_to_process a reactiveVal that contains the different assays that will be used in the module

R/server_module_workflow_config.R

@@ -30,7 +30,7 @@ server_module_workflow_config <- function(id) {
             output$tabs <- renderUI({
                 if (n_steps() > 0) {
                     lapply(seq_len(n_steps()), function(i) {
-                        selected <- "Cells Filtering"
+                        selected <- "Samples Filtering"
                         if (!is.null(steps[[paste0("step_", i)]])) {
                             selected <- steps[[paste0("step_", i)]]
                         }
@@ -39,8 +39,9 @@ server_module_workflow_config <- function(id) {
                                 inputId = NS(id, paste0("step_", i)),
                                 label = paste0("Step ", i),
                                 choices = c(
-                                    "Cells Filtering",
-                                    "Features Filtering"
+                                    "Samples Filtering",
+                                    "Features Filtering",
+                                    "Log Transformation"
                                 ),
                                 selected = selected,
                                 width = "90%"