zlskidmore
commented
2 years ago The current waterfall() function cannot do this, however I have an improved one (I plan on deprecating this one), that you might be able to get to do what you want.
Specifically the new one can take a coverage argument which is a named vector corresponding to each sample in order to calculate mutation burden. Further you can tell GenVisR to split up these calculations by the mutation type, see plotATally="complex"
There is a vignette for the new functionality here: https://pubmed.ncbi.nlm.nih.gov/34506690/
Can you take a look and see if the newer function can accomplish what you want? If not I'm happy to discuss further
Hi! I'm using the function waterfall from GenVisR package. As the vignette suggests, I want to change the top plot with custom values. However, I cannot find any option to modified these plot. As you see the below images, top plot seperated 3 kinds of the translational effect. those values cannot be specified and appear in gray as "Undefined".
[https://stackoverflow.com/questions/49644304/waterfall-plot-genvisr]
Q1. Is it possible to customize the Mutation Burden plot ? I want to change the Translational Effect category.
Q2. And I want to know how to decide the Translational Effect (Synonymous, Non Synonymous) by following Mutation type?? If the mutation type is "silent", the translational effect is specified as sysnonymous I think, but I'm not sure if all mutation types except "silent" are designated as nonsynonymous.
mutationData <- read.table('input5D_Group1.txt', sep='\t', header=TRUE) Samplelist <- read.table('Samplelist.txt', sep='\t', header=TRUE) clinicalData <- melt(data=Samplelist, id.vars=c("sample")) mutation_priority<- c("Missense, Splice site, Nonsense","Frameshift ins/del., Inframe ins/del.", "silent","UTR","Up, Downstream gene variant") waterfall(mutationData, fileType = "Custom", variant_class_order=mutation_priority, clinData=clinicalData, clinVarCol=c('Group1'='#5CD1E5'), mainPalette = c("Missense, Splice site, Nonsense"='#2F9D27',"Frameshift ins/del., Inframe ins/del."='#FF9436',"UTR"='#FF1493',"Up, Downstream gene variant"='#7B68EE'), sampOrder=Samplelist$sample[Samplelist$group=="Group1"], plotSamples=Samplelist$sample[Samplelist$group=="Group1"], rmvSilent=TRUE, mainDropMut=TRUE, maxGenes = 1000, section_heights=c(1, 10, 0.5), clinLegCol=3, mainXlabel=TRUE, coverageSpace=1000000)