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error with:cellchat <- netEmbedding(cellchat,slot.name = 'netP', type = "functional") #709

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double322 opened this issue Oct 12, 2023 · 0 comments

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@double322
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Hi, I'm simply trying to run the tutorial script in Rstudio, but am running into the following problem.

When running
,
I get the error message:cellchat <- netEmbedding(cellchat,slot.name = 'netP',type = "functional")
Manifold learning of the signaling networks for a single dataset
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')).

reticulate::py_install(packages = 'umap-learn')
Using virtual environment "C:/Users/18408/Documents/.virtualenvs/r-reticulate" ...

  • "C:/Users/18408/Documents/.virtualenvs/r-reticulate/Scripts/python.exe" -m pip install --upgrade --no-user umap-learn
    Requirement already satisfied: umap-learn in c:\users\18408\documents.virtualenvs\r-reticulate\lib\site-packages (0.5.4)
    Requirement already satisfied: numpy>=1.17 in c:\users\18408\documents.virtualenvs\r-reticulate\lib\site-packages (from umap-learn) (1.25.2)
    Requirement already satisfied: scipy>=1.3.1 in c:\users\18408\documents.virtualenvs\r-reticulate\lib\site-packages (from umap-learn) (1.11.3)
    Requirement already satisfied: scikit-learn>=0.22 in c:\users\18408\documents.virtualenvs\r-reticulate\lib\site-packages (from umap-learn) (1.3.1)
    Requirement already satisfied: numba>=0.51.2 in c:\users\18408\documents.virtualenvs\r-reticulate\lib\site-packages (from umap-learn) (0.58.0)
    Requirement already satisfied: pynndescent>=0.5 in c:\users\18408\documents.virtualenvs\r-reticulate\lib\site-packages (from umap-learn) (0.5.10)
    Requirement already satisfied: tqdm in c:\users\18408\documents.virtualenvs\r-reticulate\lib\site-packages (from umap-learn) (4.66.1)
    Requirement already satisfied: llvmlite<0.42,>=0.41.0dev0 in c:\users\18408\documents.virtualenvs\r-reticulate\lib\site-packages (from numba>=0.51.2->umap-learn) (0.41.0)
    Requirement already satisfied: joblib>=0.11 in c:\users\18408\documents.virtualenvs\r-reticulate\lib\site-packages (from pynndescent>=0.5->umap-learn) (1.3.2)
    Requirement already satisfied: threadpoolctl>=2.0.0 in c:\users\18408\documents.virtualenvs\r-reticulate\lib\site-packages (from scikit-learn>=0.22->umap-learn) (3.2.0)
    Requirement already satisfied: colorama in c:\users\18408\documents.virtualenvs\r-reticulate\lib\site-packages (from tqdm->umap-learn) (0.4.6)

cellchat <- netEmbedding(cellchat, type = "functional")
Manifold learning of the signaling networks for a single dataset
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')).
Could you please help me solve this issue? Thanks a lot in advance!

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