heatmap.CNA {ioncopy}

Visualization of Copy Number and CNA Calls

Description

Heatmap visualization including optional hierarchical clustering of amplicons/genes and samples.

Usage

heatmap.CNA(CNA, thres.percent=1, cluster.genes=TRUE, cluster.samples=TRUE,
type="CNA calls", method.dist="manhattan", method.link="average", mar=3, cex=0.50)

Arguments

CNA

Indicator matrix of CNAs generated by call.CNA.

thres.percent

Number between 0 and 100. Only genes with a minimum percentage of amplified and/or deleted samples are included into the heatmap.

cluster.genes

Logical value. If TRUE hierarchical cluster of genes is executed.

cluster.samples

Logical value. If TRUE hierarchical cluster of samples is executed.

type

Heatmap of copy numbers "Copy Number" or CNA calls "CNA Calls".

method.dist

Character. Method for calculation of the distance between genes/amplicons and between samples.

method.link

Character. Linkage method to calculate the distance between clusters.

mar

Numeric value. Margins for row names and column names.

cex

Numerical value. Shrinkage factor for row names and column names.

Value

Depending on "type" heatmap of CNAs (color coding: LOSS=green, NORMAL=black, GAIN=red) or heatmap of copy numbers (color coding CN<1: green, CN<2: darkgreen, CN>3: darkred, CN>4: red, CN>5: orange, CN>10: yellow).