I am trying to run UMAP in the following way:

RunUMAP(seurat_object, dims.use = 1:15, reduction.use = "pca", reduction.name = "umap", 
    reduction.key = "UMAP", n_neighbors = 30L, min_dist = 0.3, metric = "correlation")

Or just this:

RunUMAP(seurat_object, dims.use = 1:15, reduction.use = "pca")

It is giving me the error:

Error in py_get_attr_impl(x, name, silent) : AttributeError: module 'umap' has no attribute 'UMAP'

I already installed umap-learn successfully in this way: conda install -c conda-forge umap-learn and checked that Rstudio is using the same python version as is provided by default in the terminal: 3.6.5

  • 3
    $\begingroup$ You should post this on their github page as an issue, looks more like a software use or bug question rather than a bioinformatics question. $\endgroup$ – Peter May 25 '18 at 10:46

This is resolved by installing the more recent version of the code from GitHub.

git clone https://github.com/lmcinnes/umap
cd umap
pip install --user -r requirements.txt
python setup.py install --user

As Peter said, this kind of question is best directed to the Issues page on their GitHub repository.


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