phyCMD: Constructing configuration of trees in clusters and plot

In ymatts/PhyC: Clustering cancer evolutional trees

Description

Constructing configuration of trees in clusters and plot

Usage

phyCMD(obj, color = NULL, label = NULL, img.width = 200,
  img.height = 200, size = 0.15, type = "unrooted")

Arguments

obj	Object resulted from phyC.
color	Vector of color parameter of each cluster in the plot.
label	Vector of labels of trees. Default is "Tree i"(i=1,2,...).
size	Size parameter of trees to be plotted in the Euclidean space. Usually, 0 < size < 1. Default is 0.15.
type	Type of tree to be plotted. It must be one of "unrooted"(the default), "phylogram", "cladogram", "fan", "radial".
img.width(/img.height)	Image width (/ height) of the trees to be overlayed on the Euclidean space. The unit is "px". Default is 200.

Details

This function performs classical multidimensional scaling with tree distance. The resulting plot includes the trees overlayed on the Euclidean coordinates.

Value

dist Distance used for configuration

coord Coordinate of trees in the Euclidean space.

Author(s)

Yusuke Matsui & Teppei Shimamura

Examples

library(phyC)
data(ccRCC)
vaf <- lapply(vaf,function(x)x[,-(1:3)])
trees <- par.tree(vaf)
edgeList <- lapply(trees,function(x)x$edge)
edgeLenList <- lapply(trees,function(x)x$edge.length)
res <- phyC(edgeList,edgeLenList,cluster = 3,type = "h",method = "ward")
phyCMD(res)

ymatts/PhyC documentation built on May 4, 2019, 5:30 p.m.