---
name: "cnvkit-heatmap"
section: "1"
platform: "linux"
package: "cnvkit"
version: "0.9.12-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cnvkit-heatmap"
---

# cnvkit-heatmap(1)

Plot copy number for multiple samples as a heatmap.

## NAME

cnvkit\_heatmap - Plot copy number for multiple samples as a heatmap.

## DESCRIPTION

usage: cnvkit.py heatmap \[-h\] \[-c CHROMOSOME\] \[-y\]

- \[-x {m,y,male,Male,f,x,female,Female}\]

  \[--no-shift-xy\] \[-o FILENAME\] \[-b\] \[-d\] \[-v\] \[--delimit-samples\] \[-t TITLE\] filenames \[filenames ...\]

### positional arguments:

- filenames

  Sample coverages as raw probes (.cnr) or segments (.cns).

### options:

- **-h**, **--help**

  show this help message and exit

- **-c** CHROMOSOME, **--chromosome** CHROMOSOME

  Chromosome (e.g. 'chr1') or chromosomal range (e.g. 'chr1:2333000-2444000') to display. If a range is given, all targeted genes in this range will be shown, unless '--gene'/'-g' is already given.

- **-y**, **--male-reference**, **--haploid-x-reference**

  Assume inputs were normalized to a male reference (i.e. female samples will have +1 log-CNR of chrX; otherwise male samples would have **-1** chrX).

- **-x** {m,y,male,Male,f,x,female,Female}, **--sample-sex** {m,y,male,Male,f,x,female,Female}, **-g** {m,y,male,Male,f,x,female,Female}, **--gender** {m,y,male,Male,f,x,female,Female}

  Specify the chromosomal sex of all given samples as male or female. \[Default: guess each sample from coverage of X and Y chromosomes\].

- **--no-shift-xy**

  Don't adjust the X and Y chromosomes according to sample sex.

- **-o** FILENAME, **--output** FILENAME

  Output PDF file name.

### Plot aesthetics:

- **-b**, **--by-bin**

  Plot data x-coordinates by bin indices instead of genomic coordinates. All bins will be shown with equal width, no blank regions will be shown, and x-axis values indicate bin number (within chromosome) instead of genomic position.

- **-d**, **--desaturate**

  Tweak color saturation to focus on significant changes.

- **-v**, **--vertical**

  Plot heatmap with samples as X-axis (instead of Y-axis).

- **--delimit-samples**

  Add an horizontal delimitation line between each sample.

- **-t** TITLE, **--title** TITLE

  Plot title. \[Default: Range if provided, otherwise none\]