expPlotCreate (eset, modules, which, norm = c("sample", "raw", "feature"))
expPlot (epo, scores = TRUE)
expPlotColbar (epo)
ExpressionSet
or ISAExpressionSet
object. If an ExpressionSet
object is
supplied (and the norm
argument is not set to raw),
then it is normalised by calling ISANormalize
on it.
A subset of eset
is selected that corresponds to
the features included in modules
.
ISAModules
object.expPlotCreate
.expPlotCreate
returns an ISAexpPlot
object. It is a
named list and has several entries, the important ones:
expPlot
returns, invisibly, a named list with members:
x
and y
, both
numeric vectors of length two. They give the position of the actual
expression matrix on the plot.expPlotColbar
returns NULL
, invisibly.
expPlotCreate
creates an object that contains all data for
performing the image plot and returns it. The reason for not plotting
it directly is, that the size of the plot is usually different in
different cases, and the opening of the graphics device
is delayed until expPlotCreate
returns. In the returned object, the weight
and height
entries
give the optimal size of the image, in pixels.
expPlot
creates the expression plot.
expPlotColbar
plots a color bar for the expression plot.
eisa
package for other ISA
visualizations. The ExpressionView
package for an interactive
version.data(ALLModulesSmall)
library(ALL)
data(ALL)
ep <- expPlotCreate(ALL, ALLModulesSmall, 1)
ep
if (interactive()) {
expPlot(ep)
}
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