Karyotype function demonstration

[ahernank]

It would be great to have (or link to) an example notebook showcasing this function, using the API example as a starting point, and including some additional explanations. Akin to the terms of use example or the diplotype clustering blog.

[alimanfoo]

Thanks @ahernank, good idea. I think @sanjaynagi was contemplating a blog post on the new karyotype function possibly? If so we could advertise that.

[sanjaynagi]

Indeed writing a little blog post. Will aim to do it on the plane to NOLA. Making a map - can I use all vobs samples or Shall I stick to ag3?

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On Mon, 11 Nov 2024, 13:05 Alistair Miles, ***@***.***> wrote: Thanks @ahernank <https://github.com/ahernank>, good idea. I think @sanjaynagi <https://github.com/sanjaynagi> was contemplating a blog post on the new karyotype function possibly? If so we could advertise that. — Reply to this email directly, view it on GitHub <#52 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIKN6HOE3QLIPF7KEERQ64L2ACTSBAVCNFSM6AAAAABRRR4LSOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINRYGEZTINBUGQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[alimanfoo]

Cool, thanks Sanj. For a map you could use all samples out of embargo, i.e., where unrestricted_use is True.

[alimanfoo]

@sanjaynagi has a blog post up... https://www.sanjaycnagi.com/blog/2024-11-28-karyotyping/

We should make an update here and point to Sanj's blog.

[sanjaynagi]

Let me know if there's anything you want adding to the post, it was quite brief

[alimanfoo]

Let me know if there's anything you want adding to the post, it was quite brief

Thanks @sanjaynagi. I think the main question most folks will have is how to compute karyotype frequencies and visualise them. I raised an issue over on malariagen/malariagen-data-python#652 to implement some karyotype frequencies functions. I saw you also posted some code there, thanks for that. Still there's not quite enough information there for someone else to use it, e.g., the calc_allele_freq() function is used but not defined.

How about as a short term measure, you add a link in your blog post to the full notebook that you created to generate the map plot? At least that way someone adventurous can reuse your code and get some outputs.

In parallel we could work on adding karyotype frequencies functions into malariagen_data.

(We should also add a function to malariagen_data to make map pie chart plots!)

[sanjaynagi]

Let me know if there's anything you want adding to the post, it was quite brief

Thanks @sanjaynagi. I think the main question most folks will have is how to compute karyotype frequencies and visualise them. I raised an issue over on malariagen/malariagen-data-python#652 to implement some karyotype frequencies functions. I saw you also posted some code there, thanks for that. Still there's not quite enough information there for someone else to use it, e.g., the calc_allele_freq() function is used but not defined.

Woops, will add that too

How about as a short term measure, you add a link in your blog post to the full notebook that you created to generate the map plot? At least that way someone adventurous can reuse your code and get some outputs.

Yes, I will do this! update: I have done it

(We should also add a function to malariagen_data to make map pie chart plots!)

haha, definitely!

[alimanfoo]

(We should also add a function to malariagen_data to make map pie chart plots!)

malariagen/malariagen-data-python#678

[alimanfoo]

How about as a short term measure, you add a link in your blog post to the full notebook that you created to generate the map plot? At least that way someone adventurous can reuse your code and get some outputs.

Yes, I will do this! update: I have done it

Awesome, thanks!

https://colab.research.google.com/drive/1qlhygvn1N9XFn5oQgWIoQOMIzMQkSGoE?usp=sharing