<p>This is resolved by installing the more recent version of the code from GitHub.</p>

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

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

CC BY-SA 4.0
2018-05-31T00:52:35.393Z
2018-05-31T00:52:35.393Z
Scott Gigante
<p>I am trying to run <code>UMAP</code> in the following way:</p>

<pre><code>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")
</code></pre>

<p>Or just this:</p>

<pre><code>RunUMAP(seurat_object, dims.use = 1:15, reduction.use = "pca")
</code></pre>

<p>It is giving me the error: </p>

<blockquote>
  <p>Error in py_get_attr_impl(x, name, silent) : 
    AttributeError: module 'umap' has no attribute 'UMAP'</p>
</blockquote>

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

CC BY-SA 4.0
2018-05-25T10:46:49.240Z
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.
Peter
<scrnaseq><seurat><umap>
RunUMAP in Seurat not working: module 'umap' has no attribute 'UMAP'
# RunUMAP in Seurat not working: module 'umap' has no attribute 'UMAP'

(Asked by: username_0 on 2018-05-25)

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

**Tags:** scrnaseq, seurat, umap
> **Comments:**
> **username_1**: 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.  

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## 1 answers

### Answer by username_2 on 2018-05-31. Score: 1 | Accepted answer

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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