Add a couple of comments

fmicompbio · Aug 2, 2023 · 00edda0 · 00edda0
1 parent ddd9140
commit 00edda0
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Showing 4 changed files with 9 additions and 3 deletions.
diff --git a/R/makeAbundanceHeatmap.R b/R/makeAbundanceHeatmap.R
@@ -104,7 +104,10 @@ makeAbundanceHeatmap <- function(sce, assayToPlot, doCenter,
             mat, name = nm, ...
         )
     } else {
+        ## Should never end up here as the parameter is checked above
+        #nocov start
         stop("Unknown value of the settings parameter")
+        #nocov end
     }
 
 }

diff --git a/R/plotVolcano.R b/R/plotVolcano.R
@@ -34,7 +34,9 @@
     if (!is.null(groupmap)) {
         if (any(duplicated(groupmap$group))) {
             ## This should not happen
+            #nocov start
             stop("Something went wrong - duplicated group in groupmap")
+            #nocov end
         }
         bardata <- bardata %>%
             dplyr::left_join(groupmap, by = "group")

diff --git a/R/runTests.R b/R/runTests.R
@@ -67,7 +67,9 @@
     if (!is.null(groupmap)) {
         if (any(duplicated(groupmap$group))) {
             ## This should not happen
+            #nocov start
             stop("Something went wrong - duplicated group in groupmap")
+            #nocov end
         }
         sce$mergegroup <- groupmap$mergegroup[match(sce$group, groupmap$group)]
     } else {

diff --git a/R/summaryPlots.R b/R/summaryPlots.R
@@ -66,9 +66,8 @@ makeIntensityBoxplots <- function(sce, assayName, doLog, ylab) {
         gg <- gg + ggplot2::scale_y_log10()
     }
     if (length(unique(sce$group)) > 15) {
-        gg <- gg +
-            ggplot2::theme(
-                legend.text = ggplot2::element_text(size = ggplot2::rel(0.75)))
+        gg <- gg + ggplot2::theme(
+            legend.text = ggplot2::element_text(size = ggplot2::rel(0.75)))
     }
     gg
 }