clonevol (version 0.99.11)

generateFishplotInputs: Generate fishplot ready data from clonevol clonal evolution models

Description

Generate fishplot ready data from clonevol clonal evolution models

Usage

generateFishplotInputs(results, rescale = TRUE, samples = NULL)

Arguments

results:

output from infer.clonal.models

rescale:

rescale VAF such that no sum rule is violated (eg. parent should have VAF >= sum of its chilren's VAF

samples:

the names of the samples to be used in fishplot (this should be a subset of vaf.col.names parameter provided to infer.clonal.models); The order of samples provided will be prerseved in the fishplot

Examples

# NOT RUN {
  samples = c('P', 'R')
  v = data.frame(cluster=c(1,1,2,2),P=c(50,40,0,0),R=c(50,60,20,20))
  y = infer.clonal.models(variants=v, vaf.col.names=samples,
     founding.cluster=1)
  f = generateFishplotInputs(results=y)
# }
# NOT RUN {
  fishes = createFishPlotObjects(f)
  pdf(tempfile(), width=8, height=5)
  for (i in 1:length(fishes)){
    fish = layoutClones(fishes[[i]])
    fish = setCol(fish,f$clonevol.clone.colors)
    fishPlot(fish,shape="spline", title.btm="Patient", cex.title=0.5,
           vlines=seq(1, length(samples)), vlab=samples, pad.left=0.5)

  }
  dev.off()
# }
# NOT RUN {
# }