tests/testthat/readmeExample.R

In harrig12/TrackSigFreq-dev: TrackSig - cancer evolutionary trajectory estimation

# readmeExample.R

library(TrackSig)
library(ggplot2)

vcfFile = system.file(package = "TrackSig", "extdata/Example.vcf")
cnaFile = system.file(package = "TrackSig", "extdata/Example_cna.txt")
purity = 1

detectedSigs <- detectActiveSignatures(vcfFile = vcfFile, cnaFile = cnaFile,
                                       purity = purity, threshold = 0.05)

set.seed(1224)

# a warning will appear about not matching the refrence genome, this is because the
# example vcf file is generated by sampling random nucleotides, not real mutations.
traj <- TrackSig(sampleID = "example", activeInSample = detectedSigs,
                 vcfFile = vcfFile, cnaFile = cnaFile, purity = purity)

plotTrajectory(traj, linearX = T) + labs(title = "Example trajectory with linear x-axis")

nonLinPlot <- plotTrajectory(traj, linearX = F) + labs(title = "Example trajectory with non-linear x-axis")
addPhiHist(traj, nonLinPlot)