Usage
GSAheatmap(gsaRes, cutoff=5, adjusted=FALSE, ncharLabel=25, cellnote="pvalue", columnnames="full", colorkey=TRUE, colorgrad=NULL, cex=NULL)
Arguments
gsaRes
an object of class GSAres
, as returned from runGSA()
.
cutoff
an integer n, so that the top n gene sets (plus possible ties) in each directionality class will 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.
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 "pvalue"
, "rank"
, "nGenes"
or "none"
. Note that the actual heatmap will always be based on the gene set ranks.
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.