.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH CNVKIT_HEATMAP "1" "July 2023" "cnvkit.py heatmap 0.9.10" "User Commands"
.SH NAME
cnvkit_heatmap \- Plot copy number for multiple samples as a heatmap.
.SH DESCRIPTION
usage: cnvkit.py heatmap [\-h] [\-c CHROMOSOME] [\-y]
.TP
[\-x {m,y,male,Male,f,x,female,Female}]
[\-\-no\-shift\-xy] [\-o FILENAME] [\-b] [\-d] [\-v]
[\-\-delimit\-samples] [\-t TITLE]
filenames [filenames ...]
.SS "positional arguments:"
.TP
filenames
Sample coverages as raw probes (.cnr) or segments
(.cns).
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-c\fR CHROMOSOME, \fB\-\-chromosome\fR 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.
.TP
\fB\-y\fR, \fB\-\-male\-reference\fR, \fB\-\-haploid\-x\-reference\fR
Assume inputs were normalized to a male reference
(i.e. female samples will have +1 log\-CNR of chrX;
otherwise male samples would have \fB\-1\fR chrX).
.TP
\fB\-x\fR {m,y,male,Male,f,x,female,Female}, \fB\-\-sample\-sex\fR {m,y,male,Male,f,x,female,Female}, \fB\-g\fR {m,y,male,Male,f,x,female,Female}, \fB\-\-gender\fR {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].
.TP
\fB\-\-no\-shift\-xy\fR
Don't adjust the X and Y chromosomes according to
sample sex.
.TP
\fB\-o\fR FILENAME, \fB\-\-output\fR FILENAME
Output PDF file name.
.SS "Plot aesthetics:"
.TP
\fB\-b\fR, \fB\-\-by\-bin\fR
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.
.TP
\fB\-d\fR, \fB\-\-desaturate\fR
Tweak color saturation to focus on significant
changes.
.TP
\fB\-v\fR, \fB\-\-vertical\fR
Plot heatmap with samples as X\-axis (instead of
Y\-axis).
.TP
\fB\-\-delimit\-samples\fR
Add an horizontal delimitation line between each
sample.
.TP
\fB\-t\fR TITLE, \fB\-\-title\fR TITLE
Plot title. [Default: Range if provided, otherwise
none]