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theislab / cellrank_notebooks

Tutorials and examples for CellRank.
https://cellrank.org
BSD 3-Clause "New" or "Revised" License
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Real time tutorial #35

Closed Marius1311 closed 3 years ago

Marius1311 commented 3 years ago

Adds a new tutorial for the external WOT kernel.

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Marius1311 commented 3 years ago

@michalk8, would be great to hear your input, esp. wrt to the utility functions, which are kind of lengthy and I don't know how to hide them.

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michalk8 commented on 2021-06-24T15:15:39Z ----------------------------------------------------------------

Please take a look on how to cite the entries we have in our references.bib (for consistency, if you could do this also for old tutorials [in a separate PR], would be great).

This is done in Squidpy e.g. here: https://github.com/theislab/squidpy_notebooks/blob/master/docs/source/external_tutorials/tutorial_stardist.ipynb


Marius1311 commented on 2021-06-28T14:39:12Z ----------------------------------------------------------------

done.

Marius1311 commented on 2021-06-28T14:39:24Z ----------------------------------------------------------------

for other tutorials, will do this selarately.

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michalk8 commented on 2021-06-24T15:15:39Z ----------------------------------------------------------------

Remove this.


Marius1311 commented on 2021-06-28T09:34:48Z ----------------------------------------------------------------

will do once I'm done with everything else.

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michalk8 commented on 2021-06-24T15:15:40Z ----------------------------------------------------------------

If we're not going to expose the data through our API, add 1 line above with a link where to download these.


Marius1311 commented on 2021-06-28T09:35:21Z ----------------------------------------------------------------

We will expose the data though our API, this was just a temporary fix.

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michalk8 commented on 2021-06-24T15:15:40Z ----------------------------------------------------------------

Change It's no problem to do any of the computations here on the full data, you'll just have to move to a server or wait a bit longer.

to

It's not a problem for CellRank to do any of the computations here on the full data, we'd just have to wait a bit longer. or similar.


Marius1311 commented on 2021-06-28T09:36:18Z ----------------------------------------------------------------

thanks, done.

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michalk8 commented on 2021-06-24T15:15:41Z ----------------------------------------------------------------

All the figures seem small.


Marius1311 commented on 2021-06-28T13:33:13Z ----------------------------------------------------------------

I fixed this.

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michalk8 commented on 2021-06-24T15:15:42Z ----------------------------------------------------------------

Remove the TypeVar (ust use AnnData from anndata import AnnData).

Also, please keep imports in one place (top of the file).


Marius1311 commented on 2021-06-28T09:39:57Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2021-06-24T15:15:42Z ----------------------------------------------------------------

When using this later on, the colors of days are barely distinguishable.


Marius1311 commented on 2021-06-28T09:42:09Z ----------------------------------------------------------------

Ok, I'll change the color palette I used for the timepoints.

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michalk8 commented on 2021-06-24T15:15:43Z ----------------------------------------------------------------

I like this function, I'd consider adding it to the high-lvl API (supporting multiple fates/genes in a grid).


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michalk8 commented on 2021-06-24T15:15:43Z ----------------------------------------------------------------

total-counts normalized -> normalized by total counts


Marius1311 commented on 2021-06-28T10:10:07Z ----------------------------------------------------------------

thx.

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michalk8 commented on 2021-06-24T15:15:44Z ----------------------------------------------------------------

unbalances -> unbalanced


Marius1311 commented on 2021-06-28T10:10:42Z ----------------------------------------------------------------

thx.

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michalk8 commented on 2021-06-24T15:15:44Z ----------------------------------------------------------------

Re our discussion: I'd really include all these genes (for mouse, rat and human) in our code


Marius1311 commented on 2021-06-28T10:15:19Z ----------------------------------------------------------------

ok, searching for them.

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michalk8 commented on 2021-06-24T15:15:45Z ----------------------------------------------------------------

In computing -> During the computation

use mathjax for t_1


Marius1311 commented on 2021-06-28T14:41:45Z ----------------------------------------------------------------

done.

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michalk8 commented on 2021-06-24T15:15:46Z ----------------------------------------------------------------

See my above comment regarding the almost same colors for the days.


Marius1311 commented on 2021-06-28T14:42:36Z ----------------------------------------------------------------

Changed to color scale

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michalk8 commented on 2021-06-24T15:15:46Z ----------------------------------------------------------------

whether -> whereas


Marius1311 commented on 2021-06-28T14:44:50Z ----------------------------------------------------------------

Thanks for spotting this.

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michalk8 commented on 2021-06-24T15:15:47Z ----------------------------------------------------------------

Maybe also consider adding this plot to the API.


Marius1311 commented on 2021-06-28T14:45:23Z ----------------------------------------------------------------

Issue open

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michalk8 commented on 2021-06-24T15:15:47Z ----------------------------------------------------------------

Agreed, I'd just add some outline/thickness.


Marius1311 commented on 2021-06-28T14:45:32Z ----------------------------------------------------------------

done.

Marius1311 commented 3 years ago

Thanks for the review @michalk8! will go over this tomorrow and fix the last bits. I plan to upload the data to figshare.

Marius1311 commented 3 years ago

will do once I'm done with everything else.

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Marius1311 commented 3 years ago

We will expose the data though our API, this was just a temporary fix.

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Marius1311 commented 3 years ago

thanks, done.

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Marius1311 commented 3 years ago

ok.

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Marius1311 commented 3 years ago

Ok, I'll change the color palette I used for the timepoints.

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Marius1311 commented 3 years ago

thx.

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Marius1311 commented 3 years ago

thx.

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Marius1311 commented 3 years ago

ok, searching for them.

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Marius1311 commented 3 years ago

I fixed this.

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Marius1311 commented 3 years ago

done.

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Marius1311 commented 3 years ago

for other tutorials, will do this selarately.

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Marius1311 commented 3 years ago

done.

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Marius1311 commented 3 years ago

Changed to color scale

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Marius1311 commented 3 years ago

Thanks for spotting this.

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Marius1311 commented 3 years ago

Issue open

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Marius1311 commented 3 years ago

done.

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Marius1311 commented 3 years ago

All done, just need to integrate the gene sets now and implement the utility functions.

Marius1311 commented 3 years ago

Hi @michalk8, the wot tutorial is done and ready for a final round of your review! Feel free to add minor changes yourself while I'm going through the other tutorials to update the bibtex links.

michalk8 commented 3 years ago

@Marius1311 re bibtex: you don't need to put citations in (...), it's done through bibtex.

Marius1311 commented 3 years ago

Bibtex updates done.

michalk8 commented 3 years ago

Great, I will check if everything renders as it should/no warning and merge after release notes PR is done.

michalk8 commented 3 years ago

Kernel for WOT seems to die, I've disabled it for now on the CI.

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