Diagram: switches for limiting by chromosome and for disabling gene labels

[tetedange13]

Enhancement on diagram regarding #629

Default:

With --no-gene-labels on:

Closes #628. Closes #629.

[tskir]

Thanks Felix, everything looks good to me!

[tetedange13]

Commit e8470dd should implement a feature discussed here
=> Display a single chromosome instead of all on diagram (exactly same display as in tskir's comment with awk-filtered ".cnr")
=> I implemented like scatter -c, except "start", "end" are ignored from unpacked range
=> Works also with --no-gene-labels

Kind regards.
Felix.

[etal]

This code LGTM and I approve of the new feature. Without it, the way to get the same effect is by filtering the .cns and/or .cnr, as noted in the comments, to remove chromosomes or replace the gene names with -.

The metavar for -c might be better as "LABEL" or "NAME" ( however it appears in other commands) rather than "RANGE" to reduce the temptation to type a basepair-level range.

[tetedange13]

Hi @etal,

Thanks for your code review !
=> I decided to not set metavar= parameter at all
=> This way this part from cnvkit.py diagram --help is pretty self-explanatory:

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

Looking good to you?
Have a nice day.
Felix.

[etal]

All LGTM now