GenVisR to generate waterfall plot with clinical data: Waterfall plot is not annotating the clinical data

Question

[tanbiswas6]

Hi

I want to use GenVisR to generate oncoplot with clinical data. Though I am able to generate waterfall plot but I am not able to generate the plot using clinical data. Below is my code:

myVars <- fread("batch3_with_VAF.txt")
myVars <- myVars[,.(`Tumor_Sample_Barcode`, `Hugo_Symbol`, `Variant_Classification`, `HGVSp_Short`)]
setnames(myVars, c("sample", "gene", "mutation", "amino acid change"))

myHierarchy <- data.table("mutation"=c("Nonsense_Mutation", "Frame_Shift_Del", "Frame_Shift_Ins", "In_Frame_Del", "splice_site_del", "Splice_Site", "Missense_Mutation", "splice_region", "rna"), color=c("#FF0000", "#00A08A", "#F2AD00", "#F98400", "#5BBCD6", "#046C9A", "#D69C4E", "#000000", "#446455"))

plotData <- Waterfall(myVars, mutationHierarchy = myHierarchy)

pdf(file="Figure_try.pdf", height=8, width=12)
drawPlot(plotData)
dev.off()

myClinical <- fread("clinical_data.txt")
myClinical <- myClinical[,.(`Tumor_Sample_Barcode`, `Gleason_Score`, `PSA`)]
setnames(myClinical, c("sample", "Gleason_Score", "PSA"))
myClinical[,sample := gsub("IITK-P+","",sample)]

head(myClinical)
sample Gleason_Score                    PSA

   <char>        <char>                 <char>
1:  01-TD           GS9      more_than_hundred
2:  02-TD           GS8      more_than_hundred
3:  03-TD           GS8 more_than_five_hundred
4:  04-TD           GS7 more_than_five_hundred


myClinicalColors <- c("GS6"="#798E87", "GS7"="#C27D38", "GS8"="#CCC591", "GS9"="#76ABE2", "GS10"="#29211F", "more_than_fifteen"="#A6FF80", "more_than_hundred"="#9C964A", "more_than_five_hundred"="#85D4E3")

clinicalData <- Clinical(inputData = myClinical, palette = myClinicalColors, legendColumns = 2)
plotData <- Waterfall(myVars, mutationHierarchy = myHierarchy, clinical = clinicalData)

pdf(file="Figure_2_my.pdf", height=8, width=12)
drawPlot(plotData)
dev.off()

I am getting the same waterfall plot with no annotation of clinical data. Please let me know hoe to solve this.

Regards,
Tanay