Functions to perform transformations on the matrix used for PlotHeatmap.
Transform.no(label = " ")Transform.Z(label = "z score", center = TRUE, scale = TRUE)
Transform.VST(label = "VST")
Transform.logFC(label = "log2 FC", LFC.fun = NULL, columns = NULL, ...)
A function that transforms a matrix.
label that is used for the heatmap legend
perform centering when computing Z scores (see scale)
perform scaling when computing Z scores (see scale)
function to compute log fold changes (default: PsiLFC, other viable option: NormLFC)
which columns (i.e. samples or cells) to use as reference when computing log fold changes (see details)
further parameters passed down to LFC.fun
These functions should be used as transform parameter to PlotHeatmap. Available data transformations are
transform=Transform.Z(): compute z scores for each row; you can omit the usual centering or scaling by setting the respective parameters to false; see scale
transform=Transform.VST(): do a variance stabilizing transformation using vst
transform=Transform.logFC(): compute log2 fold changes to one or several reference columns; see below how to define them; fold changes are computed using the lfc package)
transform=Transform.no(): do not transform
The label to be used in the heatmap legend can be changed by specifying the label parameter.
For Transform.logFC, columns can be given as a logical, integer or character vector representing a selection of the columns (samples or cells).