Merge pull request #10 from Nanostring-Biostats/ProtqcVignette

modify plot in the vignette and add plot factor in code
Nanostring-Biostats · Sep 30, 2020 · 141db54 · 141db54
2 parents 4ec7fd7 + c2584fa
commit 141db54
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diff --git a/DSPPlugProtQC/eval-normalization-options-vignette.docx b/DSPPlugProtQC/eval-normalization-options-vignette.docx
diff --git a/DSPPlugProtQC/evaluate_normalization_options.R b/DSPPlugProtQC/evaluate_normalization_options.R
@@ -1,16 +1,17 @@
 ### functions to draw plots helping select normalization factors:
 # note: this code assumes the input of ERCC-normalized data for nCounter output
 
-
+# Please enter additional factor(s) you would like to plot:
+plot_factor <- c("Enter factor Here" ,"etc")
 
 # main function called by DSP-DA:
 main <- function(dataset, segmentAnnotations, targetAnnotations, outputFolder) {
 
   #### preliminaries ----------------------------------
 
   # which columns of segmentAnnotations to color plots by:
-  # colorby = choose_annotation_columns(annot = segmentAnnotations)
-  colorby <- c("ScanName", "SegmentName")
+       colorby <- intersect(c("ScanName", "SegmentName", plot_factor),
+                       colnames(segmentAnnotations))
 
   #  define the color scheme:
   cols <- assign_colors(annot = segmentAnnotations[, colorby, drop = FALSE])