subHeatmap: ntp heatmap

In MolecularPathologyLab/MmCMS: Calling CMS for mouse tissue

ntp heatmap

Description

Heatmap with marker genes and class labels.

Usage

subHeatmap(
  emat,
  res,
  templates,
  keepN = TRUE,
  labRow = NULL,
  classCol = getOption("subClassCol"),
  heatCol = NULL,
  ...
)

Arguments

emat	a numeric matrix with row features and sample columns.
res	a data frame, result from ntp function.
templates	data frame with two columns; class (factor or numeric) and probe (character).
keepN	a logical or numeric vector specifying which samples to keep.
labRow	a character specifying templates column used for labeling features.
classCol	a character vector specifying class colors.
heatCol	a character vector specifying heatmap colors (must be an even number).
...	additional arguments passed to image.

Details

subHeatmap provides a simple heatmap with samples and genes ordered according to subtype. The column bar indicates prediction p-values.

Value

a raster heatmap to visualize template feature expression.

MolecularPathologyLab/MmCMS documentation built on Oct. 18, 2023, 10:42 p.m.