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JBrowse2:Default 'Track labels' should be set to "Offset" instead of "Overlapping" #22

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sdash-github opened this issue Aug 7, 2023 · 2 comments

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@sdash-github
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It is commonly seen that the features are sometimes hidden behind the track labels in the view-window in JB2. The remedy for this is to go to triple-line-stack and set track labels to 'Offset' instead of the default 'Overlapping'. In my opinion, if we set the Offset as default it will be a desirable ux.
Hint for reproducing: start a JB2 instance of PB in an incognito window, add a linear genome, and zoom in to the feature reaosonably large to see the overlapping effect.
Adding screenshot to explain the overlapping vs. offset effect:
Screen Shot 2023-08-07 at 11 46 02 AM
For @adf-ncgr and @ctcncgr to check if this can be achieved in the JB2 config.

@adf-ncgr
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adf-ncgr commented Aug 8, 2023

I think I agree with this as a good default (I didn't actually know you could change it). Looks like setting property
"trackLabels": "offset",
in the "views" section of the config is all that's needed.

@adf-ncgr
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adf-ncgr commented Aug 9, 2023

OK, so I think I was probably wrong about it being a simple matter of tweaking the config file that is served; but it can be done with respect to programmatically specified invocations such as we make with linkouts. I've done a proof of concept with the linkout to JBrowse for BaileyII, try going to https://www.peanutbase.org/tools/gcv/gene;peanutbase=arahy.BaileyII.gnm1.ann1.mikado.chr15G1570
and access JBrowse for any of the genes from Bailey in the top query track (click gene glyph to get the linkouts).
IMHO it is not an ideal solution, and might be worth following up with JBrowse developers as to configurable defaults for some of these properties, but we could do it this way for the time being. Let me know if it seems to do what you wanted and if so I can apply to linkouts for other genomes as well.

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