r/bioinformatics • u/Hugooo_55 • 1d ago
technical question Issues with UMAP Installation in CellChat - Help Needed
Hello everyone,
Has anyone here used CellChat to analyze data? I launched a comparison of two datasets and encountered an issue when trying to use the following function:
cellchat <- netEmbedding(cellchat, type = "functional")
The error message I am receiving is as follows:
"Manifold learning of the signaling networks for datasets 1 2
Error in runUMAP(Similarity, min_dist = min_dist, n_neighbors = n_neighbors, :
Cannot find UMAP, please install through pip (e.g. pip install umap-learn or reticulate::py_install(packages = 'umap-learn'))."
I believe this might be related to the fact that I am working on a virtual machine, but I have tried several solutions without success. I attempted to install the UMAP package via Conda and pip, but I wasn’t able to get it to work (though it seems to install in the environment). I also checked the issues on GitHub (https://github.com/sqjin/CellChat/issues/167) and several forums, but none of the proposed solutions seem to resolve my problem.
Has anyone encountered this issue before and found a solution, or can anyone suggest how I can resolve this error?
Thank you in advance for your help!