viewTrees: Visualize the trees

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

Visualize the trees

Description

Visualize the trees

Usage

viewTrees(
  phyloTree,
  tree.format = "S4",
  normal.node = "NORMAL",
  group = NULL,
  group.colors = NULL,
  title = "Cancer",
  showBootstrap = TRUE,
  hexpand_ratio = 0.3
)

Arguments

phyloTree	phyloTree: The tree is in Parenthetic format.
tree.format	the format of tree, S4 or list. Default is S4.
normal.node	the sample name of normal sample in the tree.
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.
showBootstrap	whether showing the bootstrap values. Default is TRUE.
hexpand_ratio	hexpand ratio. see hexpand

Value

a ggtree object

Examples

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

# plot CNA trees without colored samples.
plotCNAtree(dist = dist)

# create a list to indicate the sample groups.
grp <- 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))
)

plotCNAtree(dist = dist, grp = grp)

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