API on website not showing up

[justinejacobi]

Hi mira!

It appears that the API reference or links to functions on the user guide website are not working.

Also, since the API isn't working right now, can you explain in a little more detail how the pointwise mutual information (between modalities) is calculated per cell?

Thank you!
-Justine

[AllenWLynch]

Hi Justine, Thank you for calling this issue with the website to our attention! Every API link is indeed gone at the moment, and I will try to fix that promptly. In the meantime, pointwise mutation information was calculated as shown here: https://en.wikipedia.org/wiki/Pointwise_mutual_information, in this function: https://github.com/cistrome/MIRA/blob/main/mira/tools/joint.py#L26 Between topics, the marginal distribution for some topic is the probability of sampling that topic across all cells (so the average topic contribution across all cells). The important part of PMI is that the expectation of PMI per observation is the MI between random variables. Allen

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________________________________ From: jjj123 ***@***.***> Sent: Tuesday, March 19, 2024 3:03 PM To: cistrome/MIRA ***@***.***> Cc: Subscribed ***@***.***> Subject: [cistrome/MIRA] API on website not showing up (Issue #43) Hi mira! It appears that the API reference or links to functions on the user guide website are not working. Also, since the API isn't working right now, can you explain in a little more detail how the pointwise mutual information (between modalities) is calculated per cell? Thank you! -Justine — Reply to this email directly, view it on GitHub<#43>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AE43JPF6C5JDOXFZKETKZOLYZCKYPAVCNFSM6AAAAABE6HRLXSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGE4TKOBYGU4DEMY>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[justinejacobi]

Perfect, thank you!