Killer feature request: plotting mode

[diego-rt]

I've been discussing with a colleague about the best way to produce some publication-quality plots.

There are a number of libraries capable of handling publication-quality plots for most common formats such as gene annotation (GFF), transcriptomics and epigenomics tracks (bigwig), bed files, bams, etc. Incorporating HiC, options narrow down a bit, but I guess there are options.

However, there are pretty much no options for plotting Cactus/MAF whole genome alignments and JBrowse's MAF plugin is perhaps the only competent visualizer out there, and does a superb job at displaying them. Therefore, we've been thinking it would be really useful if JBrowse had a figure-making plugin. Pretty much all the functionality is already there, only things missing are control over:

1. Removing/customizing grid lines
2. Axis and coordinate aesthetics
3. Font sizes (kind of already there through zoom level)
4. Vectorized output for further editing in illustrator, etc.

Thanks again for the great browser and apologies for yet another request!

[cmdcolin]

We currently have the "export SVG" feature that helps with creating publication-quality/vectorized outputted figures to a certain extent.

to truly achieve these goals, I sometimes think we need to translate jbrowse into R or something of that nature, or some crazy halfway point where jbrowse exports a ggplot2 script

[diego-rt]

Oh wow, the svg export functionality works pretty well! Can't believe I had missed this. I will play around with it some more. Thanks for the heads up!

Yes some sort of reproducible scripting would be nice. I was wondering if the config / session file isn't already some sort of script in a way? I think what would set jbrowse apart is that it isn't just a crude script like Gviz that you still need to take to illustrator to finish off, but rather a GUI where you can have more responsive feedback on the aesthetics and arrangement.

So maybe some sort of gallery mode/plugin where one can quickly access and switch between different "sessions" (which might correspond to different panels that one might want to make, each with a different genomic location and/or tracks), and with access to aesthetics like themes, axis, backgrounds, colors, font sizes, etc. Since it's saved as some kind of session, one could later come back and it would be reproducible and one could make adjustments or updates.