BGmix (version 1.32.0)

plotTrace: Trace plots for BGmix output.

Description

Trace plots are plotted for all scalar parameters. Optionally, traces are plotted for parameters indexed by genes, but for selected genes only.

Usage

plotTrace(res, q.beta = T, q.sig = T, q.z = T, ind.genes = (1:3))

Arguments

res

list object output from 'ccTrace'

q.beta

logical. Plot trace of beta (gene effect) parameters?

q.sig

logical. Plot trace of gene variances?

q.z

logical. Plot trace of gene allocation parameters?

ind.genes

indices of genes for which to plot gene parameters.

Examples

## Note this is a very short MCMC run!
## For good analysis need proper burn-in period.
data(ybar,ss)
outdir <- BGmix(ybar, ss, c(8,8), nburn=0, niter=100, nthin=1)
tr <- ccTrace(outdir)
plotTrace(tr)
plotTrace(tr,q.beta=TRUE,q.sig=FALSE,q.z=FALSE,ind.genes=1)
plotTrace(tr,q.beta=FALSE,q.sig=FALSE,q.z=TRUE,ind.genes=sample(1:1000,5))