Functions to perform transformations on the matrix used for PlotHeatmap.
Usage
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, ...)Arguments
- label
label that is used for the heatmap legend
- center
perform centering when computing Z scores (see scale)
- scale
perform scaling when computing Z scores (see scale)
- LFC.fun
function to compute log fold changes (default: PsiLFC, other viable option: NormLFC)
- columns
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
Details
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).