Seurat: Cannot find UMAP, please install through pip (e.g. pip install umap-learn).

[surljp2012]

The package version of Seurat is 3.0.2
I tried pip install umap-learn and even
library("reticulate")
use_condaenv(condaenv="Renv", conda="/Users/user/anaconda3/bin/conda")
All showed umap is installed. But it still showed that it can not find umap.
Thank you,
Jinping

[satijalab]

Please try this command, and make sure to restart R afterwards
reticulate::py_install(packages ='umap-learn')

[surljp2012]

Thank you!
I tried and it showed:

reticulate::py_install(packages ='umap-learn')
Error in conda_python(envname = envname, conda = conda) :
conda environment r-reticulate not found

Do you know what should I do to deal with this?
Thank you,
Jinping

On Fri, Jun 28, 2019 at 9:54 AM satijalab [e-mail] wrote:

Please try this command, and make sure to restart R afterwards
reticulate::py_install(packages ='umap-learn')

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[nbartonicek]

Installed new conda, umap installed, even tried reticulate::py_install(packages ='umap-learn'), restarted R and: "Cannot find UMAP, please install through pip...".
Doesn't work.

[surljp2012]

Great!
Thank you,
Jinping

On Fri, Jun 28, 2019 at 9:54 AM satijalab [e-mail] wrote:

Please try this command, and make sure to restart R afterwards
reticulate::py_install(packages ='umap-learn')

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[rlittman16]

Hi Jinping,

Try:
reticulate::py_install(envname="Renv", packages ='umap-learn')

py_install is looking for the environment r-reticulate, but you have a different name for it.

If this doesn't work, you can create a new environment called r-reticulate with:
library(reticulate)
conda_create("r-reticulate")

[surljp2012]

Thank you so much for your suggestions!

Best wishes,
Jinping

On Mon, Jul 22, 2019 at 1:21 PM rlittman16 [e-mail] wrote:

Hi Jinping,

Try:
reticulate::py_install(envname="Renv", packages ='umap-learn')

py_install is looking for the environment r-reticulate, but you have a
different name for it.

If this doesn't work, you can create a new environment called r-reticulate
with:
library(reticulate)
conda_create("r-reticulate")

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[achamess]

Hi Jinping,

Try:
reticulate::py_install(envname="Renv", packages ='umap-learn')

py_install is looking for the environment r-reticulate, but you have a different name for it.

If this doesn't work, you can create a new environment called r-reticulate with:
library(reticulate)
conda_create("r-reticulate")

The above worked for me after many tries with different solutions.
Note: I installed umap not with conda but with pip

[timoast]

We have now added support for the UWOT R package, so you no longer need to install the python package to run UMAP in Seurat. This is currently in the develop branch, see installation instructions here

[surljp2012]

Great!

Thank you and best wishes,
Jinping

On Fri, Aug 2, 2019 at 2:45 PM achamess [e-mail] wrote:

Hi Jinping,

Try:
reticulate::py_install(envname="Renv", packages ='umap-learn')

py_install is looking for the environment r-reticulate, but you have a
different name for it.

If this doesn't work, you can create a new environment called r-reticulate
with:
library(reticulate)
conda_create("r-reticulate")

The above worked for me after many tries with different solutions.
Note: I installed umap not with conda but with pip

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