spectralMap-methods {a4Base} | R Documentation |
Methods for spectralMap
## S4 method for signature 'ExpressionSet,character' spectralMap( object, groups, makeLognormal = TRUE, mpm.args = list(row.weight = "mean", col.weight = "constant", logtrans = TRUE), plot.mpm.args = list(zoom = c(1, 2), label.tol = 10, rot = c(-1, 1), sub = "", lab.size = 0.85, col.group = pData(object)[, groups], colors = c("wheat", "darkgrey", a4palette(nlevels(pData(object)[, groups]))), col.size = 2, do.smoothScatter = TRUE), probe2gene = TRUE, addLegend = TRUE, legendPos = "topleft", ... )
object |
object of class ExpressionSet |
groups |
string indicating the name of the column in the phenoData that defines the groups |
makeLognormal |
boolean indicating whether one wants to exponentiate the
data to make them lognormally shaped ( |
mpm.args |
list of arguments that can be passed to the |
plot.mpm.args |
list of arguments that can be passed to the
|
probe2gene |
boolean indicating whether one wants to display the gene symbols
for the labeled points ( |
addLegend |
Boolean indicating whether a legend for the colors of the dots should be added. |
legendPos |
Specify where the legend should be placed. Typically either |
... |
further arguments to be passed to the methods, currently not used. |
the plot is returned invisibly
Tobias Verbeke