canopy.plottree: To plot tree inferred by Canopy

In Canopy: Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing

Description

To plot Canopy's reconstructed phylogeny. Major plotting function of Canopy.

Usage

canopy.plottree(tree, pdf, pdf.name, txt, txt.name)

Arguments

tree	input tree to be plotted
pdf	whether a pdf plot should be generated, default to be FALSE
pdf.name	name of pdf to be generated, has to be provided if pdf is to be generated
txt	whether a txt file should be generated with information on mutations along the tree branches, default to be FALSE
txt.name	name of txt to be generated, has to be provided if txt is to be generated

Value

Plot of tree structure, clonal frequency and mutation legends (pdf format).

Author(s)

Yuchao Jiang [e-mail]

Examples

data(MDA231_tree)
canopy.plottree(MDA231_tree, pdf = TRUE, pdf.name = 'MDA231_tree.pdf')

Example output

Loading required package: ape
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.1-1 (2017-07-02) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

The following objects are masked from 'package:base':

    backsolve, forwardsolve

Loading required package: maps
Loading required package: pheatmap
Loading required package: scatterplot3d

Canopy documentation built on May 1, 2019, 7:59 p.m.