plotPhyloTree {MesKit} | R Documentation |
plotPhyloTree
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 )
phyloTree |
phyloTree or phyloTreeList object generated by |
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. |
return a list of phylotree graph .
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)