heatmaps: heatmaps (using heatmaps.2 of "gplots").

In ShirinG/exprAnalysis: A package for analysing RNA-seq and expression array data

Description

This calculates the differentially expressed genes among pairwise group comparisons (one comparison at a time).

Usage

heatmaps(expmatrix, method_dist = "canberra", method_hclust = "ward.D2",
  samplecols, main = "Heatmap of genes")

Arguments

expmatrix	An input matrix with gene names as row names and sample names as column names.
method_dist	the distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". Any unambiguous substring can be given. Defaults to canberra.
method_hclust	the agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC). Defaults to ward.D2.
samplecols	Colors indicating samples' treatment group.
main	Main title for heatmap plot. Defaults to "Heatmap of genes".

Value

Returns a heatmap plot.

Examples

heatmaps(expmatrix[1:100,], samplecols = rep(c("#E41A1C", "#377EB8", "#4DAF4A", "#984EA3"), each=4))

ShirinG/exprAnalysis documentation built on May 9, 2019, 1:28 p.m.