Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-05-31T00:52:35.393Z
Answers.LastActivityDate: 2018-05-31T00:52:35.393Z
Answers.UserDisplayName: Scott Gigante
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-05-25T10:46:49.240Z
Comments.Text: 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.
Comments.UserDisplayName: Peter
Tags: <scrnaseq><seurat><umap>
Title: RunUMAP in Seurat not working: module 'umap' has no attribute 'UMAP'
ThreadText: # 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.  
  
  ---
  
  ## 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 username_1 said, this kind of question is best directed to the Issues page on their GitHub repository.
  
  
  ---
  
  