Canopy (version 1.0.0)

plotpostlikelihood: To plot posterior likelihood

Description

To plot posterior likelihood of sampled trees from MCMC. Can be used to check convergence of sampling and determine cutoff values for burnin and thinning. Used in canopy.sample.

Usage

plotpostlikelihood(sampchaink,projectname,k,numchain)

Arguments

sampchaink

list of sampled trees with $k$ subclones

projectname

name of project

k

number of subclones

numchain

number of MCMC chains with random initiations

Value

Plot of posterior likelihood of trees in subtree space with specific number of subclones (pdf format).

Examples

data(MDA231_sampchain)
k = 3
K = 3:6
sampchaink = MDA231_sampchain[[which(K == k)]]
projectname = 'MDA231'
numchain = 20
plotpostlikelihood(sampchaink, projectname, k = k, numchain)