saasCNV (version 0.3.4)

diagnosis.cluster.plot: Visualize Genome-Wide SCNA Profile in 2D Cluster Plot

Description

An optional function to visualize genome-wide SCNA Profile in log2mBAF-log2ratio 2D cluster plot.

Usage

diagnosis.cluster.plot(segs, chrs, min.snps, max.cex = 3, ref.num.probe = NULL)

Arguments

segs

a data frame containing segment location, summary statistics and SCNA status resulting from cnv.call.

chrs

the chromosomes to be visualized. For example, 1:22.

min.snps

the minimum number of probes a segment span.

max.cex

the maximum of cex a circle is associated with. See details.

ref.num.probe

integer. The reference number of probes against which a segment is compared in order to determine the cex of the segment to be displayed. Default is NULL. If NULL, It will be automatically specified as 1/100 of the number of data points.

Value

An R plot will be generated.

Details

on the main log2mBAF-log2ratio panel, each circle corresponds to a segment, with the size reflecting the length of the segment; the color code is specified in legend; the dashed gray lines indicate the adjusted baselines. The side panels, corresponding to log2ratio and log2mBAF dimension respectively, show the distribution of median values of each segment weighted by its length.

See Also

joint.segmentation, cnv.call, diagnosis.seg.plot.chr, genome.wide.plot

Examples

data(seq.data)
data(seq.cnv)

diagnosis.cluster.plot(segs=seq.cnv, 
                       chrs=sub("^chr","",unique(seq.cnv$chr)), 
                       min.snps=10, max.cex=3, ref.num.probe=1000)