plot.bayesian {sma} | R Documentation |
This function plots the results of stat.bayesian() or stat.bay.est() highlighting genes meeting userspecified criteria.
plot.bayesian(x=NULL, Mbar=x$Xprep$Mbar, lods=x$lods, type="t", spec=50, ch=NULL, col="black",...)
x |
output from stat.bayesian() or stat.bay.est() |
Mbar |
Effect estimate for each gene. |
lods |
Posterior lodsratio for each gene. |
type |
Type of criteria for highlighting genes (see details). |
spec |
Specifies cutoff etc. depending on type . |
ch |
Character with which to selected highlight genes. (Default is the gene index.) |
col |
Colour of highlighted genes. (Default is black.) |
... |
Additional graphical parameters |
If type='t', plot.bayesian() highlights the top spec genes. If type='c', plot.bayesian() highlights the genes with lods>=spec. If type='i', plot.bayesian() highlights the genes with indecies specified in spec.
Ingrid Lönnstedt ingrid@math.uu.se
data(MouseArray) ## mouse.setup <- init.grid() ## mouse.data <- init.data() ## see \emph{init.data} ## mouse.lratio <- stat.ma(mouse.data, mouse.setup) mouse.bayesian<-stat.bayesian(M=mouse.lratio$M) plot.bayesian(mouse.bayesian) plot.bayesian(mouse.bayesian,type='c',spec=0,col='blue') plot.bayesian(mouse.bayesian,type='i',spec=c(1000,2000),col='green') plot.bayesian(mouse.bayesian,type='i',spec=1:length(mouse.bayesian$lods))