Answers.Body: <p>Yes, it's possible - I've added a cluster/bin biplot a function in <a href="https://github.com/gringer/shiny_cell_browser" rel="nofollow noreferrer">my Single Cell Browser</a> application - but graphical region selection is not implemented in any of the Seurat functions.</p>
  <p>When I do this myself I prefer to use the command line interface rather than the graphical interface. You can use the <code>table</code> function within R to create count bins for multiple features at the same time:</p>
  <pre><code>&gt; table(sc.data$cluster, sc.data$sampleTag)
  </code></pre>
  <p>Annotating Seurat plots (like FeaturePlot) with other graphics is possible, but difficult. I've found it easier to fetch the raw data and create a custom display function.</p>
  
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Answers.CreationDate: 2024-11-19T03:50:40.483Z
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Body: <p>In single-cell sequencing analysis, the FeaturePlot function allows us to visualize gene expression levels across different cells, and the split.by parameter enables us to create a split view based on a categorical variable, such as cell clusters. My question is, after employing the split view in FeaturePlot with the command FeaturePlot(seurat_object, features = &quot;gene_of_interest&quot;, split.by = &quot;cluster_id&quot;), is it possible to perform cell count calculations for each cluster within the split view?
  <a href="https://i.sstatic.net/O93d4cd1.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/O93d4cd1.png" alt="enter image description here" /></a></p>
  
Tags: <scrnaseq>
Title: Cell Count Calculation in Split View Using FeaturePlot
ThreadText: # Cell Count Calculation in Split View Using FeaturePlot
  
  (Asked by: username_0 on 2024-11-19)
  
  In single-cell sequencing analysis, the FeaturePlot function allows us to visualize gene expression levels across different cells, and the split.by parameter enables us to create a split view based on a categorical variable, such as cell clusters. My question is, after employing the split view in FeaturePlot with the command FeaturePlot(seurat\_object, features = "gene\_of\_interest", split.by = "cluster\_id"), is it possible to perform cell count calculations for each cluster within the split view?
  [![enter image description here](https://i.sstatic.net/O93d4cd1.png)](https://i.sstatic.net/O93d4cd1.png)
  
  **Tags:** scrnaseq
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2024-11-19. Score: 1
  
  Yes, it's possible - I've added a cluster/bin biplot a function in [my Single Cell Browser](https://github.com/username_1/shiny_cell_browser) application - but graphical region selection is not implemented in any of the Seurat functions.
  
  When I do this myself I prefer to use the command line interface rather than the graphical interface. You can use the `table` function within R to create count bins for multiple features at the same time:
  
  ```
  > table(sc.data$cluster, sc.data$sampleTag)
  
  ```
  
  Annotating Seurat plots (like FeaturePlot) with other graphics is possible, but difficult. I've found it easier to fetch the raw data and create a custom display function.
  
  
  ---
  
  