Error in cellchat <- netEmbedding(cellchat, type = "functional") / UMAP Problems

[superman2412]

Hi,

This is regarding "Manifold and Classification learning analysis of signaling networks" in the full tutorial/vignette.

I installed umap and it seems to run fine like this:

This command: cellchat <- computeNetSimilarity(cellchat, type = "functional") also seems to run well.

However: at the following command there is an error as displayed in the screenshot.

cellchat <- netEmbedding(cellchat, type = "functional")

Can you please help me troubleshoot this?

Thank you very much for your help so far!

[superman2412]

Hi @sqjin I was wondering if there's anything you could say about this? Thank you for your help so far!

[sqjin]

@superman2412 Everything looks good. Can you open a new R studio and run use_python before loading CellChat package? Do not run 'UMAP <- import('umap, ...')'.

[superman2412]

@sqjin Unfortunately, it still does not run. I was wondering if there's anything else that could be done?

[sqjin]

@superman2412 You can check this package https://github.com/jlmelville/uwot and replace the umap function using the function from this package.

[superman2412]

@sqjin Did exactly that and it fixed the problem.

For anyone facing the same problem here's the preview of the changes made in the source code, specifically in the netEmbedding function found in the analysis.R file. Again, the forked package (with changes made) be found here:

https://github.com/superman2412/CellChat/tree/master/R

Don't forget to install and load the library of this package (https://github.com/jlmelville/uwot) before trying to run the function.

@sqjin you can now close this issue.

[RajneeshSrivastava]

Thank you both, @sqjin and @superman2412 for this working solution for NetEmbedding function. My worry is, everytime I run the set of codes to generate functional plot, i find different umap profiles for pathways as color coded for clusters. Any solution to fix this?

[sqjin]

@RajneeshSrivastava Do you run umap using 'uwot' or the other one ? Do you have the same umap for each run?

[RajneeshSrivastava]

Hi @sqjin, yes i used umap from 'uwot' as suggested. I created a local function 'NetEmbedding' with umap from 'uwot' , also used for the follow up steps.

[sqjin]

@RajneeshSrivastava Can you run the default method when running netEmbedding, i.e., "umap-learn"?

[hiraksarkar]

@sqjin , It seems runUMAP is not working, is it possible to push a new version with uwot's umap?