plotCNV: Plots a Heatmap-like Overview of the CNVs

In MatthiasLienhard/qsea: IP-seq data analysis and vizualization

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.