Answers.Body: <p>That is because SCTransform (mostly) outputs discrete values, you can check the @slot of your Seurat object.</p>
  
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Answers.CreationDate: 2020-10-06T09:00:18.060Z
Answers.Text: Thank you for your answer!Do you know why this is mostly for lower expression values?
Answers.UserDisplayName: Alexandra
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Answers.CreationDate: 2020-11-06T03:53:06.850Z
Answers.Text: It's log-scaled.
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Answers.CreationDate: 2020-10-06T08:23:09.200Z
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Body: <p>I am analyzing a rather small scRNAseq dataset (39797 features across 3522 samples) and I have observed that dots in the violin plot are plotted in one line next to each other rather than in a cloud of dots (see plot below):</p>
  <p><a href="https://i.sstatic.net/xMXtu.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/xMXtu.png" alt="enter image description here" /></a></p>
  <p>I am just wonndering what the reason might be for this?</p>
  <p>I have followed the Integration and Label Transfer tutorial using SCTransform (<a href="https://satijalab.org/seurat/v3.1/integration.html" rel="nofollow noreferrer">https://satijalab.org/seurat/v3.1/integration.html</a>). After the integration process I switched back to the SCT assay, which should contain the normalized counts. For plotting I used the following command:
  VlnPlot(..., assay = &quot;SCT&quot;, slot = &quot;data&quot;), again specifying to use the normalized counts.</p>
  <p>Can someone explain me why this is the case?</p>
  <p>Thank you already in advance!</p>
  
Tags: <scrnaseq><seurat>
Title: Seurat Violin Plot: Why do dots align in one row?
ThreadText: # Seurat Violin Plot: Why do dots align in one row?
  
  (Asked by: username_0 on 2020-10-06)
  
  I am analyzing a rather small scRNAseq dataset (39797 features across 3522 samples) and I have observed that dots in the violin plot are plotted in one line next to each other rather than in a cloud of dots (see plot below):
  
  [![enter image description here](https://i.sstatic.net/xMXtu.png)](https://i.sstatic.net/xMXtu.png)
  
  I am just wonndering what the reason might be for this?
  
  I have followed the Integration and Label Transfer tutorial using SCTransform (<https://satijalab.org/seurat/v3.1/integration.html>). After the integration process I switched back to the SCT assay, which should contain the normalized counts. For plotting I used the following command:
  VlnPlot(..., assay = "SCT", slot = "data"), again specifying to use the normalized counts.
  
  Can someone explain me why this is the case?
  
  Thank you already in advance!
  
  **Tags:** scrnaseq, seurat
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-10-06. Score: 1
  
  That is because SCTransform (mostly) outputs discrete values, you can check the @slot of your Seurat object.
  
  > **Comments:**
  > **username_0**: Thank you for your answer!Do you know why this is mostly for lower expression values?  
  > **username_2**: It's log-scaled.  
  
  ---
  
  