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| CNVKIT_HEATMAP(1) |
User Commands |
CNVKIT_HEATMAP(1) |
NAME¶
cnvkit_heatmap - Plot copy number for multiple samples as a heatmap.
DESCRIPTION¶
usage: cnvkit heatmap [-h] [-b] [-c CHROMOSOME] [-d] [-y]
- [-x {m,y,male,Male,f,x,female,Female}] [--no-shift-xy]
- [-o FILENAME] filenames [filenames ...]
positional arguments:¶
- filenames
- Sample coverages as raw probes (.cnr) or segments (.cns).
optional arguments:¶
- -h, --help
- show this help message and exit
- -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.
- -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.
- -d, --desaturate
- Tweak color saturation to focus on significant changes.
- -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.
