Removed button to create expression heatmap. Fixed typo in parameter name for expression_heatmap function

Author: emouts

R/DEsummaryFuns.R

@@ -23,13 +23,13 @@ expression_heatmap <- function(
   top.annotation.ids = NULL,
   metadata,
   type = c('Z-score', 'Log2 Expression', 'Expression'),
-  show.columns.names = TRUE
+  show.column.names = TRUE
 ){
   heatmat <- as.matrix(expression.matrix.subset)
 
   type <- type[1]
   heatmat <- rescale_matrix(heatmat, type)
-  if(!show.columns.names){colnames(heatmat <- NULL)}
+  if(!show.column.names){colnames(heatmat <- NULL)}
 
   if(!is.null(top.annotation.ids)){
     qual.col.pals = dplyr::filter(RColorBrewer::brewer.pal.info, .data$category == 'qual')
@@ -57,16 +57,13 @@ expression_heatmap <- function(
     top.annotation <- NULL
   }
   if (type != 'Z-score'){
-    breaks <- seq(min(heatmat), 
-                  max(heatmat),
-                  (max(heatmat) - min(heatmat))/9)
-    colours = c("#FFFFFF",RColorBrewer::brewer.pal(n = 9, name = "YlOrRd"))
-  }
-  else {
-    breaks <- seq(-3,3,6/9)
+    breaks <- seq(min(heatmat), max(heatmat), (max(heatmat) - min(heatmat)) / 9)
+    colours = c("#FFFFFF", RColorBrewer::brewer.pal(n = 9, name = "YlOrRd"))
+  }else{
+    breaks <- seq(-3, 3, 6 / 9)
     colours = rev(RColorBrewer::brewer.pal(n = 10, name = "RdBu"))
-    heatmat[heatmat>3]<-3
-    heatmat[heatmat<(-3)]<- (-3)
+    heatmat[heatmat > 3] <- 3
+    heatmat[heatmat < (-3)] <- (-3)
   }
   ComplexHeatmap::Heatmap(
     matrix = heatmat,

R/DEsummaryPanel.R

@@ -46,7 +46,6 @@ DEsummaryPanelUI <- function(id, metadata){
       selectInput(ns("geneName"), "Additional genes to include:", multiple = TRUE, choices = character(0)),
       div("\nIf no genes are selected in the DE panel or here then the top 50 DE genes are chosen.\n"),
       div(style="margin-bottom:10px"),
-      actionButton(ns('goHeatmap'), label = 'Create heatmap'),
       textInput(ns('plotHeatmapFileName'), 'File name for heatmap plot download', value ='HeatmapPlot.png'),
       downloadButton(ns('downloadHeatmapPlot'), 'Download Heatmap Plot'),
 
@@ -128,15 +127,14 @@ DEsummaryPanelServer <- function(id, expression.matrix, metadata, DEresults, ann
           dplyr::arrange(dplyr::across(input[['heatmap.annotations']]))
 
         myplot <- expression_heatmap(
-          expression.matrix = subsetExpression[, meta[, 1]],
+          expression.matrix = subsetExpression[, meta[, 1], drop = FALSE],
           top.annotation.ids = match(input[['heatmap.annotations']], colnames(meta)),
           metadata = meta,
           type = input[["heatmap.processing"]],
           show.column.names = (nrow(meta) <= 20)
         )
         return(myplot)
-      }) %>%
-      bindEvent(DEresults(), input[['goHeatmap']])
+      }) 
     output[['heatmap']] <- renderPlot(heatmap.plot(), height = 800)
 
     output[['downloadHeatmapPlot']] <- downloadHandler(