Usage
consensusHeatmap(resList, method="median", cutoff=5, adjusted=FALSE, plot=TRUE, ncharLabel=25, cellnote="consensusScore", columnnames="full", colorkey=TRUE, colorgrad=NULL, cex=NULL)
Arguments
resList
a list where each element is an object of class GSAres
, as returned by the runGSA
function.
method
a character string selecting the method, either "mean"
, "median"
, "Borda"
or "Copeland"
.
cutoff
the maximum consensus score of a gene set, in any of the directionality classes, to be included in the heatmap.
adjusted
a logical, whether to use adjusted p-values or not. Note that if runGSA
was run with the argument adjMethod="none"
, the adjusted p-values will be equal to the original p-values.
plot
whether or not to draw the heatmap. Setting plot=FALSE
allows you to save the heatmap as a matrix without plotting it.
ncharLabel
the number of characters to include in the row labels.
cellnote
a character string selecting the information to be printed inside each cell of the heatmap. Either "consensusScore"
, "medianPvalue"
, "nGenes"
or "none"
. Note that the actual heatmap will always be based on the consensus scores.
columnnames
either "full"
(default) or "abbr"
to use full or abbreviated column labels. Will save some space for the heatmap if set to "abbr"
colorkey
a logical (default TRUE
), whether or not to display the colorkey. Will save some space for the heatmap if turned off.
colorgrad
a character vector giving the color names to use in the heatmap.
cex
a numeric, to control the text size.