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I want to perform a violin plot from a Seurat object and I rather have vertical lines. How can I stop this and rather have a standard Violin plot?

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Seurat::VlnPlot(object, features=c("LTA", "LTB"), group.by = "group",
    pt.size = 0)

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  • $\begingroup$ Why have you set the point size to zero? I expect that would stop the points from displaying on the plot. $\endgroup$
    – gringer ♦
    Commented May 12, 2022 at 2:29

1 Answer 1

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I believe the reason is simply LTA and LTB not being expressed (or their expression not being detected due to technical limitations). If you would set the pt.size argument to something else than 0, you would see a big blob of dots at point 0.0 (depending on the number of cells/data points).

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