compareTree {MesKit} | R Documentation |
Compares two phylogenetic trees and returns a detailed report of several distance methods
compareTree( phyloTree1, phyloTree2, plot = FALSE, min.ratio = 1/20, show.bootstrap = FALSE, use.tumorSampleLabel = FALSE )
phyloTree1 |
A phyloTree object generated by |
phyloTree2 |
A phyloTree object generated by |
plot |
Logical (Default: FALSE). If TRUE, two trees will be plotted on the same device and their similarities will be shown. |
min.ratio |
Double, Default 1/20. If min.ratio is not NULL, all edge length which are smaller than min.ratio*the longest edge length will be reset as min.ratio*longest edge length. |
show.bootstrap |
Logical (Default: FALSE). Whether to add bootstrap value on internal nodes. |
use.tumorSampleLabel |
Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' by 'Tumor_Sample_Label'. |
A vector containing the following tree distance methods by R package phangorn Symmetric.difference Robinson-Foulds distance KF-branch distance the branch score distance (Kuhner & Felsenstein 1994) Path.difference difference in the path length, counted as the number of branches Weighted.path.difference difference in the path length, counted using branches lengths
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") phyloTree1 <- getPhyloTree(maf$V402, method = "NJ") phyloTree2 <- getPhyloTree(maf$V402, method = "MP") compareTree(phyloTree1, phyloTree2) compareTree(phyloTree1, phyloTree2, plot = TRUE)