From 2578f6881d12540c0120a115c877515ce7816133 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 15 Jan 2020 08:54:34 +0100
Subject: [PATCH] change colormap when proportion

---
 DESCRIPTION           |  2 +-
 NAMESPACE             |  2 ++
 R/plottingFunctions.R | 10 +++++++++-
 3 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 684dcc2..ff9d146 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: analysePeaks
 Title: Compare, annotate your peaks
-Version: 1.0.2
+Version: 1.0.3
 Authors@R: 
     person(given = "Lucille",
            family = "Lopez-Delisle",
diff --git a/NAMESPACE b/NAMESPACE
index 516576a..2fdb400 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -18,6 +18,8 @@ importFrom(GenomicRanges,findOverlaps)
 importFrom(GenomicRanges,flank)
 importFrom(GenomicRanges,mcols)
 importFrom(GenomicRanges,start)
+importFrom(RColorBrewer,brewer.pal)
+importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,rainbow)
 importFrom(grDevices,rgb)
 importFrom(graphics,barplot)
diff --git a/R/plottingFunctions.R b/R/plottingFunctions.R
index e23a743..79495bd 100644
--- a/R/plottingFunctions.R
+++ b/R/plottingFunctions.R
@@ -511,6 +511,8 @@ plotAllBarPlotForCategoriesFromMyGR <- function(myGRs, nameOfColWithCate,
 #' @param plotProportion logical whether to display the pheatmap 1, 2, and 4 should be plot as proportion of pheatmap 3 and 5 (default is FALSE)
 #' @return Plot but do not return anything
 #' @importFrom pheatmap pheatmap
+#' @importFrom RColorBrewer brewer.pal
+#' @importFrom grDevices colorRampPalette
 #' @export
 plotAllPheatmapsFor2CategoriesFromMyGR <- function(myGRs, nameOfColWithCate1,
                                                    cateNames1, what1,
@@ -609,9 +611,13 @@ plotAllPheatmapsFor2CategoriesFromMyGR <- function(myGRs, nameOfColWithCate1,
       t1 <- t1 / t2
       t1[is.nan(t1)] <- 0
       number_format <- "%.2f"
+      breaks <- seq(0, 1, length.out = 101)
+      colors.name <- "PiYG"
     } else {
       line2 <- paste0(sum(t1), " peaks")
       number_format <- "%d"
+      breaks <- NA
+      colors.name <- "RdYlBu"
     }
     # We plot it
     pheatmap::pheatmap(t1, cluster_rows = F, cluster_cols = F,
@@ -619,7 +625,9 @@ plotAllPheatmapsFor2CategoriesFromMyGR <- function(myGRs, nameOfColWithCate1,
                                      "\nset:", stringSet, "\nref:", nameOfRef),
                        display_numbers = T,
                        number_format = number_format,
-                       fontsize = fontsize)
+                       fontsize = fontsize,
+                       breaks = breaks,
+                       color = colorRampPalette(rev(brewer.pal(n = 7, name = color.name)))(100))
   }
 }