--- a
+++ b/R/addonsVar.R
@@ -0,0 +1,71 @@
+###########################################################
+### ADDITIONAL VARIABLE DEFINITIONS
+###########################################################
+
+# Colors for 3 main pathways
+pathColor = c("B-cell receptor"="#f12da0",
+              "Reactive oxygen species"="#7073b0",
+              "Apoptosis (BH3)"="#efa62b",
+              "Other"="grey")
+              
+# Colors for type of drug
+typeColor = c("FDA approved"="#23b14d",
+              "clinical development/\ntool compound"="#a349a3")
+
+# Assignment of diseases to cell of origin
+diagAmt = list(
+    `B-cell origin` = c("CLL","MCL","MZL","LPL","B-PLL","HCL","HCL-V","FL"),
+    `T-cell origin` = c("T-PLL","Sezary","PTCL-NOS"),
+    `Myeloid origin`= c("AML"),
+    `Healthy`       = c("hMNC"))
+    
+# Colors for cell of origin
+colDiagL = c("B-cell origin"="skyblue",
+    "T-cell origin"="chocolate1",
+    "Myeloid origin"="yellowgreen",
+    "Healthy"="seashell4")
+
+# Colors for diseases
+colDiagS = c(`CLL`="pink", #  WH replaced "violetred" by "pink"
+    `MCL`="darkorchid",
+    `MZL`="royalblue4",
+    `LPL`="cornflowerblue",
+    `B-PLL`="darkturquoise",
+    `HCL`="cyan4",
+    `HCL-V`="mediumaquamarine",
+    `FL`="darkseagreen2",
+    `T-PLL`="darkgoldenrod1",
+    `Sezary`="brown3",
+    `PTCL-NOS`="saddlebrown",
+    `AML`="olivedrab",
+    `hMNC`="black")
+    
+## colours to annotate sample features (molecular or clinical) in heatmap
+sampleColors <- list(
+  `del 17p13`  = c(`0`   = "#f8f8f8", `1` = "darkorchid4"),
+  del11q22.3   = c(`0`   = "#f8f8f8", `1` = "darkorchid4"),
+  del13q14     = c(`0`   = "#f8f8f8", `1` = "darkorchid4"),
+  TP53         = c(`0`   = "#f8f8f8", `1` = "darkred"),
+  p53          = c(`0`   = "#f8f8f8", `1` = "darkgreen"),
+  ATM          = c(`0`   = "#f8f8f8", `1` = "darkgoldenrod3"),
+  `trisomy 12` = c(`0`   = "#f8f8f8", `1` = "darkgreen"),
+  SF3B1        = c(`0`   = "#f8f8f8", `1` = "darkblue"),
+  NOTCH1       = c(`0`   = "#f8f8f8", `1` = "darkgoldenrod3"),
+  PRPF8        = c(`0`   = "#f8f8f8", `1` = "darkorchid4"),
+  NRAS         = c(`0`   = "#f8f8f8", `1` = "darkgoldenrod3"),
+  KRAS         = c(`0`   = "#f8f8f8", `1` = "darkgoldenrod3"),
+  `KRAS | NRAS`= c(`0`   = "#f8f8f8", `1` = "darkgoldenrod3"),
+  pretreated   = c(`yes` = "firebrick2", `no` = "#f8f8f8"),
+  alive        = c(`yes` = "#f8f8f8", `no` = "black"),
+  sex          = c(`m`   = "royalblue4", `f` = "maroon"))
+
+
+# Custom made order of drugs
+mainDrOrd = c("D_164","D_030","D_082","D_003","D_002","D_166","D_036","D_079",
+              "D_071","D_035","D_050","D_020","D_163","D_078","D_162","D_077",
+              "D_075","D_045","D_032","D_074","D_012","D_033","D_023","D_083",
+              "D_172","D_029","D_024","D_017","D_063","D_034","D_015","D_021",
+              "D_165","D_004","D_040","D_001","D_081","D_048","D_060","D_039",
+              "D_067","D_169","D_084","D_025","D_010","D_006","D_159","D_056",
+              "D_008","D_127","D_141","D_149","D_049","D_007","D_054","D_013",
+              "D_066","D_011","D_168","D_167","D_043","D_041","D_053","D_CHK")