Usage
gsHeatmap(eset, ind, filename, columns = NULL, colnames = NULL,
col = NULL, annot = NULL, scale.row = FALSE, key = TRUE,
bline = NULL)
Arguments
eset
An ExpressionSet containing normalized, summarized
gene expression data. ind
Numeric vector indicating which rows of the
ExpressionSet to use. filename
The filename for the heatmap and associated key.
columns
Numeric vector indicating which columns of the
ExpressionSet to use. If NULL, all columns will be
used. colnames
Character. Substitute column names for the heatmap. If
NULL, the sampleNames will be used.
col
A vector of colors to use for the heatmap. If NULL, the
bluered function will be used. annot
A matrix or data.frame containing gene symbols to annotate the heatmap.
This will normally be extracted automatically from the 'fit' object passed to geneSetPage.
If there is no annotation in the fit object, then the probe IDs will be used instead.
scale.row
Boolean. Should the data be scaled by row? Defaults to
FALSE.
key
Boolean. Should a key be produced that shows the numeric range
for the colors of the heatmap? Defaults to TRUE.
bline
A numeric vector, usually extracted from a contrast matrix,
used to sweep the mean baseline sample means from the heatmap data.
The end result will be a heatmap in which the colors correspond to log fold
changes from the baseline samples.