search

eweitz / ideogram

Chromosome visualization for the web
https://eweitz.github.io/ideogram
Other
286 stars 72 forks source link

Is there a way to zoom in or out ideograms to check overlapped annotations? #333

Open Tong-Chen opened 1 year ago

Tong-Chen commented 1 year ago

Thanks for this great tool.

When multiple annotations are too close together (like within 10000 bases) in one chromosome as shown in https://eweitz.github.io/ideogram/annotations-tracks, only one of them could be visible. Is there any way to zoom in on one part or on the whole picture, so that these annotations can be shown?

Currently, I try to separate very close annotations into separate tracks as if they are in different groups (like pathogenic, and benign in the above example link). But this is not the best way or this could not solve all cases. I wonder if you could help to supply some hints or function updates?

Thanks!

Tong Chen

eweitz commented 1 year ago

Hi Tong, take a look at paralog neighborhoods, which address a similar use case. The HOXA1 view in gene leads ideogram also shows paralog neighborhoods (sometimes called paralogy regions). Hovering over the pink overlay annotations there shows a tooltip with brief data on genomically clustered features that are too close together to see with typical triangles beside the chromosome.

I hesitate to add zooming in Ideogram.js, as that strongly overlaps with mature products like igv.js and JBrowse that focus on small regions. However, integrations between Ideogram and those other genome browsers might suit your use case. Additionally, if something like paralog neighborhoods seem valuable, maybe that feature could be refined and generalized for use cases like yours.

Let me know your thoughts! Also, could you tell me where you're using Ideogram? Knowing more about groups and applications using Ideogram helps guide my development.

Tong-Chen commented 1 year ago

Thanks for your quick response. I have checked this paralog show before but ignored the hover box. This does give detailed information on all genes in this local region.

I am also using IGV.js which could show very close genes. This also could show neighbor genes clearly. Before I just thought if there is any way to accomplish this job just be ideogram.js. I also checked the brush function which is close to some content.

I am using ideogram.js to check if several genes could form gene clusters in the IMP website.

Thanks again for this development and answers.

Tong