[FEAT] - Normalisation skeleton

R/interface_module_box_readQFeatures.R

@@ -57,7 +57,7 @@ box_readqfeatures_ui <- function(id) {
                 ),
                 checkboxInput(
                     inputId = NS(id, "singlecell"),
-                    label = "Single cell data (WIP)",
+                    label = "Single cell data",
                     value = FALSE
                 ),
                 actionButton(

R/interface_module_normalisation_tab.R

@@ -0,0 +1,96 @@
+#' normalisation tab (section) ui builder
+#'
+#' @return A shiny tagList object that contains the normalisation tab UI components
+#' @rdname INTERNAL_interface_module_normalisation_tab
+#' @keywords internal
+#'
+#' @importFrom shiny fluidRow NS actionButton icon uiOutput
+#' @importFrom shinydashboardPlus box
+#' @importFrom htmltools tagList
+#' @importFrom shinyBS bsTooltip
+#'
+interface_module_normalisation_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"
+        ),
+        box(
+        title = "Normalisation",
+        status = "primary",
+        width = 12,
+        solidHeader = TRUE,
+        collapsible = FALSE,
+        fluidRow(
+            box(
+                title = "Prior Distribution",
+                status = "primary",
+                width = 5,
+                solidHeader = TRUE,
+                collapsible = TRUE,
+                withSpinner(plotlyOutput(outputId = NS(id, "prior_dist")),
+                    type = 6,
+                    color = "#3c8dbc"
+                )
+            ),
+            box(
+                title = "Post Distribution",
+                status = "primary",
+                width = 5,
+                solidHeader = TRUE,
+                collapsible = TRUE,
+                withSpinner(plotlyOutput(outputId = NS(id, "post_dist")),
+                    type = 6,
+                    color = "#3c8dbc"
+                )
+            ),
+            box(
+                title = "Normalisation Settings",
+                status = "primary",
+                width = 2,
+                solidHeader = TRUE,
+                collapsible = TRUE,
+                selectInput(inputId = NS(id, "method"),
+                    label = "method",
+                    choices = c(2, 10),
+                    selected = 2
+                ),
+                numericInput(inputId = NS(id, "pseudocount"),
+                    label = "Pseudocount",
+                    value = 0,
+                    min = 0,
+                    step = 1
+                )
+            )
+        )
+    ),
+        actionButton(
+            NS(id, "export"),
+            "Save the processed assays",
+            icon("hand-pointer", class = "fa-solid"),
+            width = "100%",
+            class = "load-button"
+        ),
+        shinyBS::bsTooltip(
+            id = NS(id, "export"),
+            title = paste("Write the processed assays to the QFeatures object.",
+                "This is needed to proceed to the next steps.",
+                sep = " "
+            ),
+            trigger = "hover",
+            placement = "top"
+        )
+    )
+}

R/server_dynamic_workflow.R

@@ -46,6 +46,10 @@ server_dynamic_workflow <- function(input, output, session) {
                         interface_module_log_transform_tab(
                             paste0("log_transform_", i)
                         )
+                    } else if(global_rv$workflow_config[[i]] == "Normalisation") {
+                        interface_module_normalisation_tab(
+                            paste0("normalisation_", i)
+                        )
                     }
                 )
             })
@@ -66,6 +70,10 @@ server_dynamic_workflow <- function(input, output, session) {
                 server_module_log_transform_tab(paste0("log_transform_", i),
                     step_number = i
                 )
+            } else if(global_rv$workflow_config[[i]] == "Normalisation") {
+                server_module_normalisation_tab(paste0("normalisation_", i),
+                    step_number = i
+                )
             }
         })
     })

R/server_module_normalisation_tab.R

@@ -0,0 +1,41 @@
+#' Server for the module normalisation tab
+#'
+#' @param id module id
+#' @return The server logic for the normalisation tab
+#' @rdname INTERNAL_server_module_normalisation_tab
+#' @keywords internal
+#'
+#' @importFrom shiny moduleServer updateSelectInput observeEvent eventReactive is.reactive
+#' @importFrom MultiAssayExperiment getWithColData
+#'
+server_module_normalisation_tab <- function(id, step_number) {
+    moduleServer(id, function(input, output, session) {
+        assays_to_process <- eventReactive(input$reload, {
+            error_handler(page_assays_subset,
+                component_name = "Page assays subset",
+                qfeatures = global_rv$qfeatures,
+                pattern = paste0("_(QFeaturesGUI#", step_number - 1, ")")
+            )
+        })
+
+        processed_assays <- reactive({
+            return(assays_to_process())
+        })
+
+        observeEvent(input$export, {
+            req(processed_assays())
+            loading(paste("Be aware that this operation",
+                "can be quite time consuming for large data sets",
+                sep = " "
+            ))
+            error_handler(
+                add_assays_to_global_rv,
+                component_name = "Add assays to global_rv",
+                processed_qfeatures = processed_assays(),
+                step_number = step_number,
+                type = "normalisation"
+            )
+            removeModal()
+        })
+    })
+    }

R/server_module_workflow_config.R

@@ -41,7 +41,8 @@ server_module_workflow_config <- function(id) {
                                 choices = c(
                                     "Samples Filtering",
                                     "Features Filtering",
-                                    "Log Transformation"
+                                    "Log Transformation",
+                                    "Normalisation"
                                 ),
                                 selected = selected,
                                 width = "90%"

R/utils_global.R

@@ -348,7 +348,8 @@ add_assays_to_global_rv <- function(processed_qfeatures, step_number, type) {
 #' @return `QFeatures` object with the log transformed assays
 #' @rdname INTERNAL_log_transform_qfeatures
 #' @keywords internal
-#' @importFrom QFeatures logTransform QFeatures colData
+#' @importFrom QFeatures logTransform QFeatures
+#' @importFrom SummarizedExperiment colData
 #' 
 
 log_transform_qfeatures <- function(qfeatures, base, pseudocount) {