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]