plotBasic: Basic plots of BGmix parameters and data.
In BGmix: Bayesian models for differential gene expression

Description Usage Arguments Details Value Author(s) Examples

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.

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

`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)?

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

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

Alex Lewin

## 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)