Customize display of coverage depth as XYCoverage with log scale

[thomasvangurp]

I like the ability to add a "histograms" option for displaying bam tracks when zoomed out. However, I struggle to configure the display of said histograms in the same way as I can with a normal bigwig track. For example, consider this view: I have tried to configure "histograms" with the same options as the blue bigwig track displayed below in the following fashion:

  "histograms": {
    "description": "coverage depth",
    "min": 0,
    "height": 100,
    "color": "goldenrod",
    "clip_marker_color": "red",
    "binsPerBlock": 200,
    "scale": "log",
    "type": "JBrowse/View/Track/Wiggle/XYPlot",
    "storeClass": "JBrowse/Store/SeqFeature/BigWig",
   ...
  },

So I tried setting type to XYPlot and scale to log. Alas, without results. Any pointers would be appreciated.

[cmdcolin]

This is indeed a limitation of coverage histograms to not have all full featured bigwig configurations but certainly it could be very nice to have all these options!

[thomasvangurp]

I would like to start contributing instead of just asking. @cmdcolin Could you please provide some pointers to the files / methods that would need to be adjusted for this to work?

[cmdcolin]

I haven't looked into it very much but my impression is that maybe re-publish the track config as a bigwig track type. This can use the "replace" message publish/subscribe event system in JBrowse. I can dig into more details perhaps later but that is the basic idea that I would have. In this sense, the function is kind of similar between swapping SNPCoverage and Alignments2 back and forth

[nathanhaigh]

I'd also like to have some of the features of BigWig tracks in the histograms e.g. mouse-over displaying the coverage.

[loraine-gueguen]

Another addition: it would be nice to be able to scale the coverage histograms like the XYPlot (e.g. "autoscale"="local") xref: https://sourceforge.net/p/gmod/mailman/message/36428645/