plotHeatmap: present a heatmap

In nickytong/GenAnalysis: Genomic Analysis

Description

Constructing a heatmap can be divided into 3 steps: (1) prepare column bars using prepcolbar() function: specify colorbar color schemes (2) subsetting main matrix for gene selection and sample selection using subsetMainMat() (3) transform main matrix including scaling, gene/sample clustering, and ordering. this step follows (2) with smat and can be done with transform_smat() (4) present heatmap (specify main heatmap colors)

Usage

plotHeatmap(smat_tx, colbar, rowbar = NULL,
  color = colorpalette2colvec("blueyellow"), ncolor = 60,
  colBarSel = NULL, oma = c(2, 1, 3, 11) + 0.1, plot = TRUE,
  cexRow = NULL, cexCol = NULL, labCol = NULL, labRow = NULL,
  Kcol = NULL, Krow = NULL, labColpal = "set1", labRowpal = "set2",
  labRowcolor = NULL, ...)

Arguments

colbar	column bar object as returned by prepcolbar(): need to add option for colbar=NULL, no colbar case
rowbar	row bar object as returned by prepcolbar(). Default is NULL, meaning no rowbar
color	color vector for expression data
ncolor	number of colors to be interpolated based on color parameter
colBarSel	a vector to select a subset of column bars; this should be a subset of colnames of pheno data (also colnames of colbar)
oma	oma passed to par()
plot	whether to plot the heatmap
...	additional parameters to heatmat

Value

mapL list with additional attributes to reconstruct heatmap to reconstruct, use: with(attributes(phm), ...)

nickytong/GenAnalysis documentation built on July 20, 2019, 8:57 a.m.