[WIP] - starting ggridges implementation

NAMESPACE

@@ -19,6 +19,9 @@ importFrom(RColorBrewer,brewer.pal)
 importFrom(SummarizedExperiment,assay)
 importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,ggplot)
+importFrom(ggridges,geom_density_ridges)
 importFrom(htmltools,HTML)
 importFrom(htmltools,a)
 importFrom(htmltools,br)
@@ -40,6 +43,7 @@ importFrom(plotly,add_annotations)
 importFrom(plotly,add_histogram)
 importFrom(plotly,add_trace)
 importFrom(plotly,config)
+importFrom(plotly,ggplotly)
 importFrom(plotly,hide_colorbar)
 importFrom(plotly,layout)
 importFrom(plotly,plot_ly)

R/interface_module_normalisation_tab.R

@@ -6,7 +6,7 @@
 #'
 #' @importFrom shiny fluidRow NS actionButton icon uiOutput
 #' @importFrom shinydashboardPlus box
-#' @importFrom htmltools tagList
+#' @importFrom htmltools tagList h2
 #' @importFrom shinyBS bsTooltip
 #'
 interface_module_normalisation_tab <- function(id) {
@@ -34,32 +34,21 @@ interface_module_normalisation_tab <- function(id) {
         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,
+                width = 9,
                 solidHeader = TRUE,
                 collapsible = TRUE,
-                withSpinner(plotlyOutput(outputId = NS(id, "post_dist")),
+                withSpinner(plotlyOutput(outputId = NS(id, "density_plot")),
                     type = 6,
                     color = "#3c8dbc"
                 )
             ),
             box(
                 title = "Normalisation Settings",
                 status = "primary",
-                width = 2,
+                width = 3,
                 solidHeader = TRUE,
                 collapsible = TRUE,
                 selectInput(inputId = NS(id, "method"),
@@ -75,7 +64,11 @@ interface_module_normalisation_tab <- function(id) {
                     "quantiles.robust",
                     "vsn"),
                     selected = "center.median"
-                )
+                ),
+                h2("Plot options"),
+                selectInput(inputId = NS(id, "color"),
+                    label = "Color by",
+                    choices = NULL)
             )
         )
     ),

R/server_module_normalisation_tab.R

@@ -28,6 +28,27 @@ server_module_normalisation_tab <- function(id, step_number) {
             )
         })
 
+        output$density_plot <- renderPlotly({
+            req(processed_assays())
+            density_by_sample_plotly(
+                qfeatures = processed_assays(),
+                color = input$color
+            )
+            # error_handler(
+            #     density_by_sample_plotly,
+            #     component_name = "Density by sample plotly",
+            #     qfeatures = processed_assays(),
+            #     color = input$color)
+        })
+
+        observe({
+            req(processed_assays())
+            updateSelectInput(session,
+                "color",
+                choices = colnames(colData(processed_assays()))
+            )
+        })
+
         observeEvent(input$export, {
             req(processed_assays())
             loading(paste("Be aware that this operation",
@@ -43,5 +64,6 @@ server_module_normalisation_tab <- function(id, step_number) {
             )
             removeModal()
         })
+
     })
-    }
+}

R/utils_global.R

@@ -379,4 +379,39 @@ normalisation_qfeatures <- function(qfeatures, method) {
     })
     names(el) <- names(qfeatures)
     QFeatures(el, colData = colData(qfeatures))
-    }
+    }
+
+
+#'A function that return a plot of the densities of intensities by sample
+#' 
+#' @param qfeatures `QFeatures` object
+#' @param color `str` colname of the column of colData to use as color
+#' @return a plotly object
+#' 
+#' @rdname INTERNAL_density_by_sample_plotly
+#' @keywords internal
+#' @importFrom plotly ggplotly
+#' @importFrom ggplot2 ggplot aes
+#' @importFrom ggridges geom_density_ridges
+
+density_by_sample_plotly <- function(qfeatures, color) {
+
+    combined_df <- data.frame(intensity = numeric(), sample = character())
+    for (assayName in names(qfeatures)) {
+        assayData <- assay(qfeatures[[assayName]])
+
+        intensities <- as.vector(assayData)
+        sampleNames <- rep(colnames(assayData), each = nrow(assayData))
+
+        assay_df <- data.frame(intensity = intensities, sample = sampleNames)
+
+        combined_df <- rbind(combined_df, assay_df)
+    }
+    print(colData(qfeatures)[combined_df$sample, color])
+    combined_df$color <- colData(qfeatures)[combined_df$sample, color]
+
+    plot <- ggplot(combined_df, aes(x = intensity, y = sample, fill = color)) +
+        geom_density_ridges()
+
+    ggplotly(plot)
+}