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eweitz / ideogram

Chromosome visualization for the web
https://eweitz.github.io/ideogram
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Support for structural rearrangements #316

Open jmur14 opened 1 year ago

jmur14 commented 1 year ago

Could ideogram support circular diagrams to depict ring chromosomes?

eweitz commented 1 year ago

This is intriguing. Could you briefly explain how this would be useful to support in Ideogram?

jmur14 commented 1 year ago

Cytogeneticists have to rely on something like cydas.org to draw the chromosomal abnormality like a ring and the terminal deletions on both ends of the chromosome. However, there is no easy way to depict in picture form what the resultant abnormal ring would look like. There are no tools to create the ring from the abnormal ideogram.

image

eweitz commented 1 year ago

Thanks, the explanation and image are helpful. I see the image shows a linear chromosome, yet you'd like a circular ring, thus your feature request here. I sympathize with a desire for cytogenetic convention and more biological realism, even though the linear form might abstractly convey key information.

For convenient reference, here's a ring chromosome image I found from Garsed DW, Holloway AJ, Thomas DM. Cancer-associated neochromosomes: a novel mechanism of oncogenesis. Bioessays. 2009 Nov;31(11):1191-200. doi: 10.1002/bies.200800208. PMID: 19795405.

ring_chromosome_example

Is the ring chromosome in B above basically what you're looking for? If not, can you attach some reference image(s) here, for how you'd ideally like these ring chromosomes to look?

jmur14 commented 1 year ago

What you are showing is perfect. I guess the main reason for my request would be for comparing with real chromosomes for publication purposes.

[image: image.png]

On Thu, Feb 2, 2023 at 7:40 PM Eric Weitz @.***> wrote:

Thanks, the explanation and image are helpful. I see the image shows a linear chromosome, yet you'd like a circular ring, thus your feature request here. I sympathize with a desire for more biological realism, even though the linear form might abstractly convey key information.

Beyond more realism, could you elaborate what value in seeing the ring chromosomes as a circular diagram? Is it easier to understand scientifically? What about a ring chromosome would be hard to convey in linear form that's better conveyed in circular form?

For convenient reference, here's a ring chromosome image https://onlinelibrary.wiley.com/cms/asset/bd3ce207-892d-476c-9efa-3557e0f67609/mfig001.jpg I found from Garsed DW, Holloway AJ, Thomas DM. Cancer-associated neochromosomes: a novel mechanism of oncogenesis. Bioessays. 2009 Nov;31(11):1191-200. doi: 10.1002/bies.200800208. PMID: 19795405.

[image: ring_chromosome_example] https://user-images.githubusercontent.com/1334561/216481687-b650348c-2238-4680-8067-e62013aadbf3.jpeg

Is the ring chromosome in B above basically what you're looking for? If not, can you attach some reference image(s) here, for how you'd ideally like these ring chromosomes to look?

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