BGmix (version 1.32.0)

plotBasic: Basic plots of BGmix parameters and data.

Description

Plots gene effects and variances versus their corresponding data sufficient statistics (to show the effect of smoothing and shrinkage). Also plots "volcano plots": posterior probabilities of being classified in each mixture component versus the log fold change parameters.

Usage

plotBasic(res, ybar, ss, q.mean = T, q.diff = T, q.sig = T, q.volcano = T)

Arguments

res

list object output from 'ccParams'

ybar

ybar data (see BGmix help for details)

ss

ss data (see BGmix help for details)

q.mean

logical. Include mean plot?

q.diff

logical. Include log fold change plot?

q.sig

logical. Include variance plot?

q.volcano

logical. Include volcana plot (posterior classification v. fold change)?

Value

No value is returned to R. Results from BGmix model are output to files.

Details

Note this plotting function is designed for model output from the unpaired differential expression design.

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)
params <- ccParams(outdir)
plotBasic(params,ybar,ss)