Draws a scatter plot between means from a pairwise comparison. Colours according to PMA calls and identifies 'signficant' genes yielded by a filtering
Usage
## S3 method for class 'pairwise.comparison'
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.