Add gene_labels and labels to plot_genes()

[leehart]

Resolves #407.

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[alimanfoo]

Looking good...

[alimanfoo]

Hi @leehart, couple of comments...

One very small request, would it be possible to add just a little more vertical padding around the text labels? Particularly the negative strand gene labels are touching the gene rectangles, would be good to have a little padding.

The other request is that ultimately this will be needed as part of functions like plot_h12_gwss() where there is a genes track plotted below some other data track. So basically, could you add a gene_labels parameter to all functions like this, i.e., where plot_genes() is called internally?

[leehart]

@alimanfoo How does this padding look to you?

Ideally I'd like a more robust mechanism for accommodating these labels, because this is currently tailored to the default height of the plot, i.e. 120, so specifying a different height, e.g. height=240, results in a skewed layout, e.g.

[alimanfoo]

@alimanfoo How does this padding look to you?

Looks good!

Ideally I'd like a more robust mechanism for accommodating these labels, because this is currently tailored to the default height of the plot, i.e. 120, so specifying a different height, e.g. height=240, results in a skewed layout, e.g.

Thanks @leehart, I think it's probably ok for now, generally unlikely to need to vary the height of this track by much.

[alimanfoo]

Hi @leehart, could we rename the labels param to gene_labelset? That way when the parameter appears in functions like plot_h12_gwss() it will be more obvious that the parameter will apply to the genes track.

[codecov]

Codecov Report

Attention: Patch coverage is 12.50000% with 28 lines in your changes missing coverage. Please review.

Project coverage is 94.57%. Comparing base (af6bac1) to head (cc1ce67).
Report is 79 commits behind head on master.

Files with missing lines	Patch %	Lines
malariagen_data/anoph/genome_features.py	6.66%	28 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #653      +/-   ##
==========================================
- Coverage   95.19%   94.57%   -0.62%     
==========================================
  Files          40       40              
  Lines        4144     4187      +43     
==========================================
+ Hits         3945     3960      +15     
- Misses        199      227      +28     

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[leehart]

Looks like codecov/patch wants some test coverage for the new gene_labels param. Will do.

[alimanfoo]

Looks like codecov/patch wants some test coverage for the new gene_labels param. Will do.

Cool, thanks @leehart. Happy to be merged once codecov/patch passes.