plotPhyloTree: plotPhyloTree

In MesKit: A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations

Description

plotPhyloTree

Usage

plotPhyloTree(
  phyloTree,
  patient.id = NULL,
  branchCol = "mutType",
  show.bootstrap = TRUE,
  min.ratio = 1/20,
  signaturesRef = "cosmic_v2",
  min.mut.count = 15,
  use.tumorSampleLabel = FALSE,
  show.scale.bar = FALSE,
  scale.bar.x = NULL,
  scale.bar.y = NULL
)

Arguments

phyloTree	phyloTree or phyloTreeList object generated by getPhyloTree function.
patient.id	Select the specific patients. Default NULL, all patients are included.
branchCol	Specify the colors of branches Default 'mutType'. Other options: "mutSig" for coloring branches by branch mutation signature;
show.bootstrap	Logical (Default: TRUE). Whether to add bootstrap value on internal nodes.
min.ratio	Double. Default 1/20. If min.ratio is not NULL, all edge length of a phylogenetic tree should be greater than min.ratio*the longest edge length. If not, the edge length will be reset as min.ratio*longest edge length.
signaturesRef	Signature reference,Users can upload their own reference. Default "cosmic_v2". Option:"exome_cosmic_v3","nature2013".
min.mut.count	The threshold for the variants in a branch. Default 15.
use.tumorSampleLabel	Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Sample_Label'.
show.scale.bar	Logical (Default: FALSE). Whether to show scale bar.This function adds a horizontal bar giving the scale of the branch lengths to a plot on the current graphical device.
scale.bar.x	The x location of scale bar.
scale.bar.y	The y location of scale bar.

Value

return a list of phylotree graph .

Examples

maf.File <- system.file("extdata/", "CRC_HZ.maf", package = "MesKit")
clin.File <- system.file("extdata/", "CRC_HZ.clin.txt", package = "MesKit")
ccf.File <- system.file("extdata/", "CRC_HZ.ccf.tsv", package = "MesKit")
maf <- readMaf(mafFile=maf.File, clinicalFile = clin.File, ccfFile=ccf.File, refBuild="hg19")

phyloTree <- getPhyloTree(maf, patient.id = 'V402')
plotPhyloTree(phyloTree)

MesKit documentation built on March 28, 2021, 6 p.m.