plotCNV: Plots a Heatmap-like Overview of the CNVs

View source: R/qsea.plots.R

plotCNVR Documentation

Plots a Heatmap-like Overview of the CNVs

Description

This function plots the Copy Number Variations (CNVs) of the samples in a heatmap like representation. Amplified regions are depicted in red, whereas deletions are depicted green, and CNV free regions blue. The samples are ordered by an hierarchical clustering.

Usage

plotCNV(qs, dist = c("euclid", "cor")[1], clust_method = "complete",
            chr = getChrNames(qs), samples =getSampleNames(qs),
            cex = 1, labels = c(TRUE, TRUE,TRUE, TRUE), naColor = "darkgrey",
            indicateLogFC = TRUE )

Arguments

qs

a qseaSet object (mandatory)

dist

distance measure for clustering. dQuoteeuclidian or dQuotecorrelation based (1-cor)

clust_method

method to be passed to hclust

chr

vector of chromosomes to be depicted

samples

samples for which CNVs are depicted

cex

font size of labels

labels

Boolean vector of length four (bottom, left, top, right), specifying the sides of the map to be labeled

naColor

Color for regions without CNV information

indicateLogFC

indicate the CNV logFC values in the legend

Value

This function returns the pairwise distances of the CNV profiles, on which the clustering is based on.

Author(s)

Mathias Lienhard

Examples

qs=getExampleQseaSet()
plotCNV(qs, labels=c(FALSE, TRUE, TRUE, FALSE))

MatthiasLienhard/qsea documentation built on March 22, 2023, 1:15 p.m.