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

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!


1 Answer 1


That is because SCTransform (mostly) outputs discrete values, you can check the @slot of your Seurat object.

  • $\begingroup$ Thank you for your answer!Do you know why this is mostly for lower expression values? $\endgroup$
    – Alexandra
    Oct 6, 2020 at 9:00
  • $\begingroup$ It's log-scaled. $\endgroup$
    – burger
    Nov 6, 2020 at 3:53

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