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