cn.region.heatmap: A Function for Creating a Heatmap of DNA Copy Number Data
In MVisAGe: Compute and Visualize Bivariate Associations

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

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"))

`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").

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)