Scroll to navigation



cnvkit_heatmap - Plot copy number for multiple samples as a heatmap.


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:

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


show this help message and exit
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.
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.
Tweak color saturation to focus on significant changes.
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).
Specify the chromosomal sex of all given samples as male or female. (Default: guess each sample from coverage of X and Y chromosomes).
Don't adjust the X and Y chromosomes according to sample sex.
Output PDF file name.
September 2022 cnvkit heatmap 0.9.9