NAME

       cnvkit_diagram - Draw copy number (log2 coverages, segments) on chromosomes as a diagram.

           If both the raw probes and segments are given, show them side-by-side on
           each chromosome (segments on the left side, probes on the right side).

DESCRIPTION

       usage: cnvkit.py diagram [-h] [-s SEGMENT] [-c CHROMOSOME] [-t THRESHOLD]

       [-m MIN_PROBES] [-y]
              [-x   {m,y,male,Male,f,x,female,Female}]  [--no-shift-xy]  [-o  FILENAME]  [--title
              TITLE] [--no-gene-labels] [filename]

   positional arguments:
       filename
              Processed coverage data file (*.cnr), the output of the 'fix' sub-command.

   options:
       -h, --help
              show this help message and exit

       -s SEGMENT, --segment SEGMENT
              Segmentation calls (.cns), the output of the 'segment' command.

       -c CHROMOSOME, --chromosome CHROMOSOME
              Chromosome to display, e.g. 'chr1' (no chromosomal range allowed)

       -t THRESHOLD, --threshold THRESHOLD
              Copy number change threshold to label genes. [Default: 0.5]

       -m MIN_PROBES, --min-probes MIN_PROBES
              Minimum number of covered probes to label a gene.  [Default: 3]

       -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 sample's chromosomal sex as male or female. (Otherwise guessed  from  X
              and Y coverage).

       --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:
       --title TITLE
              Plot title. [Default: sample ID, from filename or -i]

       --no-gene-labels
              Disable gene_name labels on plot (useful when a lot of CNV were called).