table of contents
| CNVKIT_HEATMAP(1) | User Commands | CNVKIT_HEATMAP(1) |
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]
| July 2023 | cnvkit.py heatmap 0.9.10 |