Added returnData argument to plotFoldChange

Author: travis-m-blimkie

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pathlinkR
 Type: Package
 Title: Analyze and interpret RNA-Seq results
-Version: 1.5.2
+Version: 1.5.3
 Authors@R: c(
     person("Travis", "Blimkie", email = "travis.m.blimkie@gmail.com", role = "cre", comment = c(ORCID = "0000-0001-8778-8627")),
     person("Andy", "An", email = "andy@hancocklab.com", role = "aut")

R/plotFoldChange.R

@@ -65,6 +65,8 @@
 #' @param rowAngle Angle of row text, defaults to 0.
 #' @param rowCenter Whether to center column text. The default is FALSE, but it
 #'   should be set to TRUE if vertical column name (e.g. `rowAngle=90`).
+#' @param returnData Boolean (FALSE). Whether to draw the heatmap (default) or
+#'   return the underlying matrix.
 #'
 #' @return A heatmap of fold changes for genes of interest; an "ggplot" class
 #'   object
@@ -145,7 +147,8 @@ plotFoldChange <- function(
         colAngle=90,
         colCenter=TRUE,
         rowAngle=0,
-        rowCenter=FALSE
+        rowCenter=FALSE,
+        returnData=FALSE
 ) {
 
     stopifnot(
@@ -357,6 +360,10 @@ plotFoldChange <- function(
         rowSplit <- var
     }
 
+    if (returnData) {
+        return(list("matFC" = matFC, "matP" = matP))
+    }
+
     draw(
         Heatmap(
             matrix=matFC,

man/plotFoldChange.Rd

@@ -14,3 +14,21 @@ test_that("fold change heatmaps are working with some customization", {
         )
     )
 })
+
+test_that("argument 'returnData' is working.", {
+    set.seed(1)
+
+    data("exampleDESeqResults")
+
+    expect_type(
+        plotFoldChange(
+            inputList = exampleDESeqResults,
+            pathName = "Interferon alpha/beta signaling",
+            hideNonsigFC = FALSE,
+            invert = TRUE,
+            clusterColumns = TRUE,
+            returnData = TRUE
+        ),
+        "list"
+    )
+})