Man page - cnvkit-heatmap(1)
Packages contains this manual
- cnvkit-import-theta(1)
- cnvkit-coverage(1)
- cnvkit-metrics(1)
- cnvkit-import-seg(1)
- cnvkit-export(1)
- cnvkit-breaks(1)
- cnvkit-fix(1)
- cnvkit-segmetrics(1)
- cnvkit-batch(1)
- cnvkit-import-rna(1)
- cnvkit-bintest(1)
- cnvkit-diagram(1)
- cnvkit-call(1)
- cnvkit-autobin(1)
- cnvkit-access(1)
- cnvkit-antitarget(1)
- cnvkit-sex(1)
- cnvkit-segment(1)
- cnvkit-genemetrics(1)
- cnvkit-heatmap(1)
- cnvkit-target(1)
- cnvkit-import-picard(1)
- cnvkit-reference(1)
- cnvkit-scatter(1)
apt-get install cnvkit
Manual
CNVKIT_HEATMAP
NAMEDESCRIPTION
positional arguments:
options:
Plot aesthetics:
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]