Qc heatmap (#390)

* dna rna heatmap added

* dna rna heatmap added

* x label heatmap fixed

* x label heatmap fixed

* results display simplified

* fix no results scenario in overview

* results display simplified

* results display simplified

Co-authored-by: Vicente <yepez@in.tum.de>
Co-authored-by: nickhsmith <smithnickh@gmail.com>

drop/modules/aberrant-expression-pipeline/OUTRIDER/Summary.R

@@ -111,12 +111,13 @@ ggplot(bcv_dt, aes(when, BCV)) +
 #' ## Results
 res <- fread(snakemake@input$results)
 
-#' Total number of expression outliers: `r nrow(res)`
+#' Total number of expression outliers: `r nrow(res)`  
 #' Samples with at least one outlier gene: `r res[, uniqueN(sampleID)]`  
 
 #'
 #' ### Aberrant samples
-#' An aberrant sample is one that has more than 0.1% of the expressed genes called as outliers.
+#' 
+#' An aberrant sample is one that has more than 0.1% of the total genes called as outliers.
 if (nrow(res) > 0) {
   ab_table <- res[AberrantBySample > nrow(ods)/1000, .("Outlier genes" = .N), by = .(sampleID)] %>% unique
   if (nrow(ab_table) > 0) {
@@ -125,25 +126,24 @@ if (nrow(res) > 0) {
   } else {
     print("no aberrant samples")
   }
-} else {
-  print('no results')
-}
+} else print("no aberrant samples")
 
 
-#' ### Results table
+#' ## Results table
 
-## Save the results table in the html folder and provide link to download
+## Save results table in the html folder and provide link to download
 file <- snakemake@output$res_html
 fwrite(res, file, sep = '\t', quote = F)
-#+ echo=FALSE, results='asis'
-cat(paste0("<a href='./", basename(file), "'>Download OUTRIDER results table</a>"))
 
-res[, pValue := format(pValue, scientific = T, digits = 3)]
-res[, padjust := format(padjust, scientific = T, digits = 3)]
 
-DT::datatable(
-  head(res, 1000),
-  caption = 'OUTRIDER results (up to 1,000 rows shown)',
-  options=list(scrollX=TRUE),
-  filter = 'top'
-)
+if(nrow(res) > 0){
+  res[, pValue := format(pValue, scientific = T, digits = 3)]
+  res[, padjust := format(padjust, scientific = T, digits = 3)]
+
+  DT::datatable(head(res, 1000), caption = 'OUTRIDER results (up to 1,000 rows shown)',
+                options=list(scrollX=TRUE), filter = 'top')
+
+} else print("no significant results")
+
+#+ echo=FALSE, results='asis'
+cat(paste0("<a href='./", basename(file), "'>Download OUTRIDER results table</a>"))

drop/modules/mae-pipeline/QC/DNA_RNA_matrix_plot.R

@@ -96,8 +96,8 @@ ann_colors[['status']] <- ann_colors[['status']][unique(c(dna_df$status, rna_df$
 
 #+ Heatmap, fig.height=6, fig.width=8
 pheatmap(qc_mat, color = color, cluster_rows = FALSE, cluster_cols = FALSE, 
-         annotation_row = dna_df, annotation_col = rna_df, annotation_colors = ann_colors, 
-         labels_row = 'DNA samples', labels_col = 'RNA samples')
+         annotation_row = dna_df, annotation_col = rna_df, annotation_colors = ann_colors,
+         labels_row = 'DNA samples', labels_col = 'RNA samples', angle_col = 0)
 
 
 #' ## Identify matching samples

drop/template/Scripts/AberrantExpression/Overview.R

@@ -84,8 +84,8 @@ DT::datatable(res, filter = 'top')
 
 #' Choose a random gene and sample to plot. Outliers are in red.
 #+ echo=TRUE
-gene <- res[1, geneID]
-sample <- res[1, sampleID]
+gene <- ifelse(nrow(res)>1, res[1, geneID], rownames(ods)[1])
+sample <- ifelse(nrow(res)>1, res[1, sampleID], colnames(ods)[1])
 
 #' ### Volcano plot
 #' setting basePlot = FALSE creates an interactive plot

drop/template/Scripts/AberrantSplicing/Overview.R

@@ -82,7 +82,7 @@ DT::datatable(res, filter = 'top')
 
 #' Get a splice site and sample of interest. Outliers are in red.
 #+ echo=TRUE
-sample <- res[1, sampleID]
+sample <- ifelse(nrow(res)>1, res[1, sampleID], colnames(fds)[1])
 siteIndex <- 4
 
 #' ### Volcano plot