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!