GMOD / jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser
https://jbrowse.org/jb2
Apache License 2.0
208 stars 62 forks source link

Improved method for visualizing inversions in synteny view? #3420

Open cmdcolin opened 1 year ago

cmdcolin commented 1 year ago

If there is an inversion, it can be nice to horizontally flip one of the views in a synteny view to "straighten it out" (can pick either top or bottom, functionally the same) but this can cause some messy rendering

Example screenshot untitled(4)

Some strategies that could help fix:

cmdcolin commented 1 year ago

Actual screenshot after horizontally flipping a region with an inversion

Screenshot from 2022-12-19 17-04-42

cmdcolin commented 1 year ago

another somewhat related visualization issue that comes up in inversions, conceptual diagram of the "problem"

untitled(2)

actual screenshot of the above (insertion/deletion both don't follow the hourglass in the below screenshot)

Screenshot from 2022-12-20 13-56-54

would need to be able to find the "point of intersect" to attempt the above, and it may be challenging and unclear whether it will really help though