Scanpy integration fails during analysis for scanpy > 1.4.1 about conos HOT 11 CLOSED

What version of scanpy do you use?

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I'm using scanpy ver. 1.4.3

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It was indeed an issue with the scanpy version. After downgrading to ver. 1.4.1 I was able to proceed with the analysis.

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I have the same issue.
Please, Can I know how I could downgrade version of Scanpy to 1.4.1?

from conos.

It was indeed an issue with the scanpy version. After downgrading to ver. 1.4.1 I was able to proceed with the analysis.

I have the same issue.
Please, Can I know how I could downgrade version of Scanpy to 1.4.1?

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Yeah, I need to get in contact with scanpy folks to fix this issue.
@DuaaAlawad , see comment to #33

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Yeah, I need to get in contact with scanpy folks to fix this issue.
@DuaaAlawad , see comment to #33
thanks .. I got the solution.

pip install scanpy==1.4.1

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Hey! Scanpy uses the umap function to find approximate knn graphs. This looks like it has something to do with the newest umap update, which was incorporated into scanpy. Maybe @ivirshup could give some insight into this?

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Thanks for the ping, I think I see the issue.

We try and get the parameters used to create the neighbor network so that we can make sure we're computing the UMAP layout on the right data, using the right methods. This requires a few parameters:

• To make sure we're using the right data, we need the representation the neighbors were calculated on, so the values of use_rep and n_pcs.
• UMAP needs to know the distance metric that was used for some cases of the layout. This would be passed as a string for the key metric. If it's a metric which takes additional arguments those would be passed in a dict under metric_kwds.

On the scanpy end of things, we could make it so your call doesn't throw an error by just assuming you used default values, but I don't think that would be a good idea. I would suggest providing those parameters when you add the neighbor graph to the AnnData object.

Here's the relevant code from scanpy: https://github.com/theislab/scanpy/blob/d8f32c040f3a5f4fc07998b269796ca58de84b40/scanpy/tools/_umap.py#L128-L150

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Thank you so much, @ivirshup ! Updated it in e7f2f37, now everything works fine.

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This fix seems to have been removed again in #45

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