diversity: Evaluating diversity and plot

In ymatts/PhyC: Clustering cancer evolutional trees

Description

Evaluating diversity and plot

Usage

diversity(obj, color = NULL, plotit = T)

Arguments

obj	Object resulted from phyC.
color	If plotit=TRUE, color parameter of each cluster in the plot.
plotit	Whether plot the diversity or not (logical).

Value

ind.div Diversity of each tree.

div Diversity of each cluster.

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")
div <- diversity(res)

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