simpleaffy (version 2.48.0)

plot.pairwise.comparison: Plots a PairComp object

Description

Draws a scatter plot between means from a pairwise comparison. Colours according to PMA calls and identifies 'signficant' genes yielded by a filtering

Usage

"plot"(x,y=NULL,labels=colnames(means(x)),showPMA=TRUE,type="scatter",...)

Arguments

x

A PairComp object

y

A PairComp object

labels

A list containing x and y axis labels

showPMA

True if PMA calls are to be identified

type

Can be 'scatter', 'ma' or 'volcano'

...

Additional arguments to plot

Details

Takes a PairComp object (as produced by pairwise.comparison and plots a scatter plot between the sample means. If PMA calls are present in the calls slot of the object then it uses them to colour the points. Present on all arrays: red; absent on all arrays: yellow; present in all some arrays; orange. In addition, if a second PairComp object is supplied, it identifies spots in that object, by drawing them as black circles. This allows, for example, the results of a pairwise.filter to be plotted on the same graph.

If type is 'scatter' does a simple scatter plot. If type is 'volcano' does a volcano plot. If type is 'ma' does an MA plot.

See Also

pairwise.comparison pairwise.filter trad.scatter.plot

Examples

  ## Not run: 
#     pc <- pairwise.comparison(eset.mas,group="group",members=c("a","b"),spots=eset)
#     pf <- pairwise.filter(pc)
#     plot(pc,pf)
#   ## End(Not run)