Parsing of color assignment for plotting from DM.R to DMRichR::proces…

…sBismark()
ben-laufer · Mar 19, 2021 · 68aa14d · 68aa14d
1 parent 58a2ab7
commit 68aa14d
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Showing 2 changed files with 9 additions and 9 deletions.
diff --git a/R/processBismark.R b/R/processBismark.R
@@ -242,6 +242,15 @@ processBismark <- function(files = list.files(path = getwd(), pattern = "*.txt.g
     stop(print(glue::glue("processBismark arguments")))
   } 
 
+  glue::glue("Assigning colors for plotting...")
+  pData <- pData(bs.filtered)
+  if(length(levels(pData[,testCovariate])) == 2){
+    pData$col <- NULL
+    pData$col[pData[,testCovariate] == levels(pData[,testCovariate])[1]] <- "mediumblue"
+    pData$col[pData[,testCovariate] == levels(pData[,testCovariate])[2]] <- "firebrick3"
+    pData(bs.filtered) <- pData
+  }
+
   print(glue::glue("processBismark timing..."))
   end_time <- Sys.time()
   print(end_time - start_time)

diff --git a/exec/DM.R b/exec/DM.R
@@ -162,15 +162,6 @@ bs.filtered <- DMRichR::processBismark(files = list.files(path = getwd(),
                                        perGroup = perGroup,
                                        sexCheck = sexCheck)
 
-glue::glue("Assigning colors for plotting...")
-pData <- pData(bs.filtered)
-if(length(levels(pData[,testCovariate])) == 2){
-  pData$col <- NULL
-  pData$col[pData[,testCovariate] == levels(pData[,testCovariate])[1]] <- "mediumblue"
-  pData$col[pData[,testCovariate] == levels(pData[,testCovariate])[2]] <- "firebrick3"
-  pData(bs.filtered) <- pData
-}
-
 glue::glue("Saving Rdata...")
 save(bs.filtered, file = "RData/bismark.RData")
 #load("RData/bismark.RData")