.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.10.
.TH CNVKIT_DIAGRAM "1" "March 2019" "cnvkit_diagram 0.9.5" "User Commands"
.SH NAME
cnvkit_diagram \- Draw copy number (log2 coverages, CBS calls) 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).
    
.SH DESCRIPTION
usage: cnvkit diagram [\-h] [\-s SEGMENT] [\-t THRESHOLD] [\-m MIN_PROBES] [\-y]
.TP
[\-x {m,y,male,Male,f,x,female,Female}] [\-\-no\-shift\-xy]
[\-o FILENAME] [\-\-title TITLE]
[filename]
.SS "positional arguments:"
.TP
filename
Processed coverage data file (*.cnr), the output of
the 'fix' sub\-command.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-s\fR SEGMENT, \fB\-\-segment\fR SEGMENT
Segmentation calls (.cns), the output of the 'segment'
command.
.TP
\fB\-t\fR THRESHOLD, \fB\-\-threshold\fR THRESHOLD
Copy number change threshold to label genes. [Default:
0.5]
.TP
\fB\-m\fR MIN_PROBES, \fB\-\-min\-probes\fR MIN_PROBES
Minimum number of covered probes to label a gene.
[Default: 3]
.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 sample's chromosomal sex as male or
female. (Otherwise guessed from X and Y coverage).
.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\-\-title\fR TITLE
Plot title. [Default: sample ID, from filename or \fB\-i]\fR