Plots and graphics


Plot probe log2 coverages and segmentation calls together. scatter Sample.cnr -s Sample.cns

The options --gene, --chromosome or --range (or their single-letter equivalents) focus the plot on the specified region: scatter Sample.cnr -s Sample.cns -r chr7 scatter Sample.cnr -s Sample.cns -r BRAF scatter Sample.cnr -s Sample.cns -r chr7:140434347-140624540

In the latter two cases, the --width (-w) argument determines the size of the chromosomal regions to show flanking the selected region.

Loss of heterozygosity (LOH) can be viewed alongside copy number by passing variants as a VCF file with the -v option. Heterozygous SNP allelic frequencies are shown in a subplot below the CNV scatter plot. (Also see the loh command, below.) scatter Sample.cnr -s Sample.cns -v Sample.vcf

The probe copy number values can also be plotted without segmentation calls: scatter Sample.cnr

This can be useful if CBS is unavailable, or for viewing the raw, un-corrected coverages when deciding which samples to use to build a profile, or simply to see the coverages without being helped/biased by the called segments.

The --trend option (-t) adds a smoothed trendline to the plot. This is fairly superfluous if a valid segment file is given, but could be helpful if CBS is not available, or if you’re skeptical of the segmentation in a region.


Plot allelic frequencies at each variant position in a VCF file. Divergence from 0.5 indicates loss of heterozygosity (LOH) in a tumor sample. loh Sample.vcf


Draw copy number (either raw probes (.cnn, .cnr) or segments (.cns)) on chromosomes as a diagram. If both the raw probes and segmentation calls are given, show them side-by-side on each chromosome (segments on the left side, probes on the right side). diagram Sample.cnr diagram -s Sample.cns diagram -s Sample.cns Sample.cnr


Draw copy number (either raw probes (.cnn, .cnr) or segments (.cns)) for multiple samples as a heatmap.

The segmentation calls alone will render much faster, and will probably be more useful to look at. heatmap *.cns heatmap *.cnr  # Slow!