cn.region.heatmap {MVisAGe}

A Function for Creating a Heatmap of DNA Copy Number Data

Description

This function creates a heatmap of DNA copy number data for a given chromosomal region.

Usage

cn.region.heatmap(cn.mat, gene.annot, plot.chr, plot.start, plot.stop,
  plot.list, sample.annot = NULL, sample.cluster = F, low.thresh = -2,
  high.thresh = 2, num.cols = 50, collist = c("blue", "white", "red"),
  annot.colors = c("black", "red", "green", "blue", "cyan"),
  plot.sample.annot = F, cytoband.colors = c("gray90", "gray60"))

Arguments

cn.mat

A matrix of gene-level DNA copy number data (rows = genes, columns = samples). DNA methylation data can also be used. Both row names (gene names) and column names (Sample IDs) must be given.

gene.annot

A three-column matrix containing gene position information. Column 1 = chromosome number written in the form 'chr1' (note that chrX and chrY should be written chr23 and chr24), Column 2 = position (in base pairs), Column 3 = cytoband.

plot.chr

The chromosome used to define the region of interest.

plot.start

The genomic position (in base pairs) where the region starts.

plot.stop

The genomic position (in base pairs) where the region stops.

plot.list

A list produced by corr.list.compute().

sample.annot

An optional two-column matrix of sample annotation data. Column 1 = sample IDs, Column 2 = sample annotation (e.g. tumor vs. normal). If NULL, sample annot will be created using the common sample IDs and a single group ('1'). Default = NULL.

sample.cluster

Logical values indicating whether the samples should be clustered. Default = FALSE.

low.thresh

Lower threshold for DNA copy number measurements. All values less than low.thresh are set equal to low.thresh. Default = -2.

high.thresh

Upper threshold for DNA copy number measurements. All values greater than high.thresh are set equal to high.thresh. Default = 2.

num.cols

Number of distinct colors in the heatmap. Default = 50.

collist

Color scheme for displaying copy number values. Default = ("blue", "white", "red").

annot.colors

Character vector used to define the color scheme for sample annotation. Default = c("black", "red", "green", "blue", "cyan").

plot.sample.annot

Logical value used to specify whether the sample annotation information should be plotted. Default = FALSE.

cytoband.colors

Character vector of length two used to define the color scheme for annotating the cytoband. Default = c("gray90", "gray60").

Examples

exp.mat = tcga.exp.convert(exp.mat)

 cn.mat = tcga.cn.convert(cn.mat)

 prepped.data = data.prep(exp.mat, cn.mat, gene.annot, sample.annot, log.exp = FALSE)

 pd.exp = prepped.data[["exp"]]

 pd.cn = prepped.data[["cn"]]

 pd.ga = prepped.data[["gene.annot"]]

 pd.sa = prepped.data[["sample.annot"]]

 output.list = corr.list.compute(pd.exp, pd.cn, pd.ga, pd.sa)

 cn.region.heatmap(cn.mat = pd.cn, gene.annot = pd.ga, plot.chr = 11,

plot.start = 0e6, plot.stop = 135e6, sample.annot = pd.sa, plot.list = output.list)