plotPhyloTree {MesKit} | R Documentation

## plotPhyloTree

### 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)

[Package MesKit version 1.4.0 Index]