Refactoring/optimization of IsoformPlot

sheynkman-lab / biosurfer

"Surf" the biological network, from genome to transcriptome to proteome and back to gain insights into human disease biology.

MIT License

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Refactoring/optimization of IsoformPlot #88

Open jsaquing opened 3 years ago

jsaquing commented 3 years ago

Goals:

more control over visual format of plotted objects
- i.e. need to better separate code that handles adding objects (abstract) to plot from code that actually adds Artists (concrete) to Figure
make it faster to generate multiple plots, potentially involving the same underlying set of transcript isoforms
- try to reuse Artists and Axes between plots if possible

jsaquing commented 3 years ago

Idea: create JSON-based format for representing all information in a plot (i.e. tracks, genomic coords of each region/marker, formatting, text) and "plotters" for different backends (e.g. Matplotlib, Bokeh) that create plots based on the JSON objects