Plots and graphics


Plot bin-level log2 coverages and segmentation calls together. Without any further arguments, this plots the genome-wide copy number in a form familiar to those who have used array CGH. scatter Sample.cnr -s Sample.cns
# Shell shorthane scatter -s{s,r}

The options --chromosome and --gene (or their single-letter equivalents) focus the plot on the specified region: scatter -s{s,r} -c chr7 scatter -s{s,r} -c chr7:140434347-140624540 scatter -s{s,r} -g BRAF

In the latter two cases, the genes in the specified region or with the specified names will be highlighted and labeled in the plot. The --width (-w) argument determines the size of the chromosomal regions to show flanking the selected region. Note that only targeted genes can be highlighted and labeled; genes that are not included in the list of targets are not labeled in the .cnn or .cnr files and are therefore invisible to CNVkit.

To create multiple region-specific plots at once, the regions of interest can be listed in a separate file and passed to the scattter command with the -l/--range-list option. This is equivalent to creating the plots separately with the -c option and then combining the plots into a single multi-page PDF.

The arguments -c and -g can be combined to e.g. highlight specific genes in a larger context:

# Show the whole chromosome, highlight two genes scatter -s{s,r} -c chr7 -g BRAF,MET
# Show a chromosome arm, highlight one gene scatter -s{s,r} -c chr5:100-50000000 -g TERT

When a chromosomal region is plotted with CNVkit’s “scatter” command , the size of the plotted datapoints is proportional to the weight of each point used in segmentation – a relatively small point indicates a less reliable bin. Therefore, if you see a cluster of smaller points in a short segment (or where you think there ought to be a segment, but there isn’t one), then you can cast some doubt on the copy number call in that region. The dispersion of points around the segmentation line also visually indicates the level of noise or uncertainty.

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.) scatter Sample.cnr -s Sample.cns -v Sample.vcf

The bin-level log2 ratios or coverages can also be plotted without segmentation calls: scatter Sample.cnr

This can be useful for viewing the raw, un-corrected coverage depths 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 the CBS dependency 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 individual bins (.cnn, .cnr) or segments (.cns)) on chromosomes as an ideogram. If both the bin-level log2 ratios and segmentation calls are given, show them side-by-side on each chromosome (segments on the left side, bins on the right side). diagram Sample.cnr diagram -s Sample.cns diagram -s Sample.cns Sample.cnr

If bin-level log2 ratios are provided (.cnr), genes with log2 ratio values beyond a fixed threshold will be labeled on the plot. This plot style works best with target panels of a few hundred genes at most; with whole-exome sequencing there are often so many genes affected by CNAs that the individual gene labels become difficult to read.

If only segments are provided (-s), gene labels are not shown. This plot is then equivalent to the heatmap command, which effectively summarizes the segmented values from many samples.


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

To get an overview of the larger-scale CNVs in a cohort, use the “heatmap” command on all .cns files: heatmap *.cns

The color range can be subtly rescaled with the -d option to de-emphasize low-amplitude segments, which are likely spurious CNAs: heatmap *.cns -d

A heatmap can also be drawn from bin-level log2 coverages or copy ratios (.cnn, .cnr), but this will be extremely slow at the genome-wide level. Consider doing this with a smaller number of samples and only for one chromosome at a time, using the -c option: heatmap *.cnr -c chr7  # Slow!

If an output file name is not specified with the -o option, an interactive matplotlib window will open, allowing you to select smaller regions, zoom in, and save the image as a PDF or PNG file.