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debbiemarkslab / EVcouplings

Evolutionary couplings from protein and RNA sequence alignments
http://evcouplings.org
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Secondary structure and numbering on contact maps #23

Open deboramarks opened 7 years ago

deboramarks commented 7 years ago

Put numbering and secondary structure logo on same axis in contact maps for better visualization.

thomashopf commented 7 years ago

The older plotting code had this feature but I removed it - the major issue with this was that the secondary structure started overlapping with the numbers depending on 1) the length of the number label or 2) the fontsize of the label. This always required manual fiddling to make the plots look nice. If this feature is to come back, it has to address these points automatically and in a satisfactory way.

aggreen commented 6 years ago

@sacdallago will re-implement this in the frontend with javascript - maybe port to the backend after new implementation.

thomashopf commented 6 years ago

This issue is just about the positioning of the number labels and the secondary structure cartoon along the x/y axes of the plots - the current solution with opposite sides is the robust and easy one since there won't be overlaps between the two. I originally had the functionality in to plot them on the same side, but that required a lot of manual fiddling. Independent of this, will be good to have the interactive contact maps in the pipeline too.

sacdallago commented 6 years ago

@thomashopf thanks for the clarification.

Most of the graphical stuff will be re-implemented anyway (there's almost no way to port py-whatever based viz to JS), so it doesn't make sense to spend too much energy in making this available through the pipeline now. Backwards (JS to pipeline) is way easier :)