plotCNAtree: plotCNAtree plots phylogenetic trees of CNAs

In qingjian1991/MPTevol: Clonal Evolutionary History and Metastatic Routines Analysis for Multiple Primary Tumors

plotCNAtree plots phylogenetic trees of CNAs

Description

The CNAs trees were constructed by MEDICC.

Usage

plotCNAtree(
  dist,
  bootstrap.rep.num = 500,
  group = NULL,
  group.colors = NULL,
  title = "Cancer",
  normal.node = "NORMAL",
  hexpand_ratio = 0.3
)

Arguments

dist	dist files that generated by MEDICC.
bootstrap.rep.num	number of bootstrap steps.
group	a list that used to indicate the sample groups
group.colors	an array indicates the colors of sample groups.
title	title of the plot.
normal.node	the sample name of normal sample in the tree.
hexpand_ratio	hexpand ratio. see hexpand

Examples

# read samples distances.
# This dist file is the output of MEDICC
dist <- system.file(package = "MPTevol", "extdata", "tree_final.dist")

# set group information
group <- list(
  NORMAL = "NORMAL",
  Breast = paste0("Breast_", 1:5),
  Coad = paste0("Coad_", 1:5),
  Lung = paste0("Lung_", 1:5),
  OveryLM = paste0("OveryLM_", 1:5),
  OveryRM = paste0("OveryRM_", 1:6),
  UterusM = paste0("UterusM_", c(1:7))
)

# set group colors
group.colors <- setNames(set.colors(n = length(group)), nm = names(group))

# built trees
tree <- plotCNAtree(
  dist = dist,
  group = group,
  group.colors = group.colors
)

tree$plot

qingjian1991/MPTevol documentation built on Jan. 30, 2023, 10:16 p.m.