Draw variants, transcript and protein.

[ielis]

• write about visualization.
• Read background

Todos:

• Title including transcript id, protein id & name
• transcript tract: get exon lengths from tx_coordinates.get_cds_regions()
• transcript track: add CDs region number
• protein track: length of gray bar: tx_coordinates.get_codon_count() this is the length of the encoding regions (Note: # codons/ 3 = # bases), make sure to align gray and transcript exactly
• protein track: each box stands for a feature protein_meta.protein_features (for pf in protein_meta.protein_features: pf.info.region # is the region of the feature)
• protein track: feature type encoded by colors pf.feature_type
• protein track: annotate box with feature name pf.info.name
• add legend displaying variant effects and feature types colors

[frehburg]

Hey @ielis,

I got started and played around with the visualization a bit and copied the image Lauren showed last time. As of now it looks like this:

This is Laurens image:

My function looks as such: draw_fig(limits, protein_limits, markers) Where limits is and array of tuples where tuple[0] is the beginning of a box on the upper line and tuple[1] is the end. protein_limits is just a 1D array of strictly increasing numbers and the boxes on the lower line are drawn with consecutive pairs taken from this list. I figured this would be sufficient, since there don't seem to be any gaps as above. Lastly, markers is also just a 1D array of x positions and I draw a little pin at that location, increasing the stem length and circle radius the more often the same x appears.

I would imagine that this method is a good starting point to develop the figure you have in mind. Visually everything can be customized to adhere more to your preferences. The bioinformatics logic can be added to give my drawing method the right inputs. Etc etc.

Please let me know what you think

[pnrobinson]

awesome!

[ielis]

Hi @frehburg the picture looks indeed awesome!
I'll write some prose into the notebook in this repo to make sure we are on the same page but overall I think this is fabulous!

I'll let you know when I'm done with the prose.

Thanks a lot! :)

[lnrekerle]

I think all that's left of this task is having a legend for the variant effect colors! @frehburg is this something you can work on?
And thank you so much for all the work you've done on the visualization!!

[pnrobinson]

I think this issue is closable if the CI problem in this PR is fixed!
#184

[pnrobinson]

@ielis @frehburg Hi Filip, I have now used this code for 70 genes and it is beautiful!
Would it be easy to add the exon chart underneath the protein as is shown in the above example? If this is simple, let's do it, but it is not a game-stopper if not.

[frehburg]

Hey Peter,

Sorry for my late reply. I think that would be possible. Let's discuss this after the AMIA if that is okay.