search

eweitz / ideogram

Chromosome visualization for the web
https://eweitz.github.io/ideogram
Other
294 stars 71 forks source link

Chromosome disappears after being clicked for some organisms #330

Closed matthewwiese closed 1 year ago

matthewwiese commented 1 year ago

I first noticed this when setting my organism to cassava; however, it is also observable in grape and green algae in the eukaryotes example. A demo gif:

ideogram

eweitz commented 1 year ago

Thanks for the clear steps to reproduce. This is a bug in handling genomes fetched directly from NCBI.

In addition to fixing this bug, I might also inline several genomes to improve load times. So specifying cassava or Manihot esculenta would automatically load the latest major genome assembly, M.esculenta_v8 (GCF_001659605.2).

Do you work with any other organisms where that would help? Also, would you mind if I asked in which organization you're using Ideogram.js?

eweitz commented 1 year ago

Fixed, thanks again for the report. Any insight on where you're using this would help Ideogram!

matthewwiese commented 1 year ago

Thanks so much for addressing this so quickly @eweitz!

I'm in Dr. Edward Buckler's lab at Cornell University. We haven't actually used Ideogram.js for anything yet - I've been looking into libraries that could be used inside Jupyter Notebooks to visualize chromosomes (which prompted #329). The interactivity afforded by a solution like Ideogram.js is particularly appealing.

Edit: And to answer your other question, I am currently working closely with cassava. However, the lab works with zea (particularly maize), tripsacum, sorghum, and many others.