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### ADDITIONAL VARIABLE DEFINITIONS

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# 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")