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Palantir for Single cell trajectory detection #493

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merged 30 commits into from Mar 21, 2019

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commented Feb 18, 2019

@falexwolf
I'm adding a wrapper for Palantir by Setty et al. (2018)
Please let me know if you have any comments

awnimo added some commits Feb 15, 2019

_palantir.py added to tools
Added Palantir functionality to Scanpy
Update _phenograph.py
updated documentation

@awnimo awnimo changed the title Palantir integration Palantir for Single cell trajectory detection Feb 26, 2019

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commented Mar 10, 2019

Thank you for this, @awnimo! I added a few small comments.

Could you move the whole code into scanpy/external/_tools, please? We'll transition to all wrapper code for external code to be in that directory. Thank you!

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awnimo added some commits Mar 11, 2019

Palantir (#493)
Updates following comments by @falexwolf
Delete _palantir.py
move _palantir.py to external/_tools at @falexwolf request
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commented Mar 11, 2019

Thank you for this, @awnimo! I added a few small comments.

Could you move the whole code into scanpy/external/_tools, please? We'll transition to all wrapper code for external code to be in that directory. Thank you!

Hey @falexwolf ,
I have completed the changes you requestedI.
Please let me know if there are any other issues.

Thank you

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awnimo added some commits Mar 12, 2019

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commented Mar 12, 2019

Hey @falexwolf,
Any other issues to fix?
Thank you

awnimo added some commits Mar 12, 2019

Parameters
----------
adata: :class:`~anndata.AnnData`

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falexwolf Mar 19, 2019

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Sorry, but there needs to be a white space between parameters and colon: adata : instead of adata: . :) Otherwise the docs will break.

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flying-sheep Mar 19, 2019

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Also you document some parameters but the function only has one.

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awnimo Mar 19, 2019

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Thank you @falexwolf and @flying-sheep !
I fixed the docs.

note: how can I check if the docs break? I usually run make html in docs to inspect the rendering, and I didn't get any flags

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falexwolf Mar 19, 2019

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Using make html is fine. Just inspect the resulting pages and you'll see that the layout is broken if something goes wrong.

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commented Mar 21, 2019

Looks good! Thank you! :)

@falexwolf falexwolf merged commit 202952d into theislab:master Mar 21, 2019

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@awnimo awnimo deleted the dpeerlab:Palantir branch Mar 21, 2019

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commented Mar 28, 2019

Hi, I am trying to use palantir. I've updated by pip install git+https://github.com/theislab/scanpy.git

when I try to import scanpy I get the following error:
ModuleNotFoundError: No module named 'scanpy.external._tools'

I'm fairly new to python packaging. Apologies if this is an issue with my install method. also not an expert with github project managment. Will gladly post this elsewhere if better.

Thanks!

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commented Mar 28, 2019

Palantir is not yet in a released version: https://scanpy.readthedocs.io/en/latest/#on-master-march-21-2019

We'll soon have 1.4.1. Until then, you need to install from GitHub as described in the installation section. :)

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commented Mar 28, 2019

Should’ve checked the docs for installation. Thanks!

@ivirshup ivirshup referenced this pull request Apr 11, 2019

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latest version error #601

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