figClassifyCMS: plot heatmap

In rpiskol/CMString: CMS classification using a selected set of genes that are profiled using the NanoStrin echnology

Description

plot heatmap with gene expression of classifier genes as well as classifications, their probabilities and phenotypic information (mutations)

Usage

figClassifyCMS(x, pred, clu.pred, sdat.sig, gclu.f, nam.ord,
  missing.genes = NULL, cex.axis.labs = 1, mutmat = NULL,
  gene.labs = TRUE, samp.labs = FALSE)

Arguments

x	list with classification results (pred, clu.pred, sdat.sig, gclu.f, nam.ord, missing.genes) [default: none]
pred	matrix of class prediction probabilities with samples in rows and classes in the columns. [default: none]
clu.pred	vector with predicted classes [default: none]
sdat.sig	matrix with gene expression values for the classifier genes with samples in genes in rows and samples in columns [default: none]
gclu.f	hierarchical clustering of classifier genes that specifies row ordering [default: none]
nam.ord	vector of sample IDs that specify column ordering of heatmap [default: none]
missing.genes	vector of genes that will be removed from the heatmap. These are usually genes that were not present in the expression data, but required by the classifier. However any other list can of IDs can be specified [default: NULL]
cex.axis.labs	numeric scaling factor for axis labels (genes, samples) [default: 1]
mutmat	matrix of numeric values that will be translated into colors and attached to the bottom of the heatmap. This can contain mutational information or any other phenotypic information [default: NULL]
gene.labs	boolean specifying whether gene labels should be plotted [default: TRUE]
samp.labs	boolean specifying whether sample labels should be plotted [default: FALSE]

Author(s)

Robert Piskol

rpiskol/CMString documentation built on May 24, 2019, 8:52 a.m.