text: user9638: 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):
  
  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!
  
  user3541: That is because SCTransform (mostly) outputs discrete values, you can check the @slot of your Seurat object.
  
original_text: 9638: <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.stack.imgur.com/xMXtu.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/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>
   3541: <p>That is because SCTransform (mostly) outputs discrete values, you can check the @slot of your Seurat object.</p>
  