minor fixes outrider summary

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

@@ -65,7 +65,7 @@ plotAberrantPerSample(ods, main = dataset_title,
 #+ countCorHeatmap, fig.height=8, fig.width=8
 plotCountCorHeatmap(ods, normalized = FALSE, colGroups = "isExternal", colColSet = "Dark2",
                     main = paste0('Raw Counts (', dataset_title, ')'))
-plotCountCorHeatmap(ods, normalized = TRUE, ,colGroups = "isExternal", colColSet = "Dark2",
+plotCountCorHeatmap(ods, normalized = TRUE, colGroups = "isExternal", colColSet = "Dark2",
                     main = paste0('Normalized Counts (', dataset_title, ')'))
 
 
@@ -110,10 +110,12 @@ ggplot(bcv_dt, aes(when, BCV)) +
 #' ## Results
 res <- fread(snakemake@input$results)
 
+#' 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 total genes called as outliers.
+#' An aberrant sample is one that has more than 0.1% of the expressed 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) {
@@ -127,9 +129,9 @@ if (nrow(res) > 0) {
 }
 
 
-#' ## Results table
+#' ### Results table
 
-## Save results table in the html folder and provide link to download
+## Save the 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'