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I was confused about the VlnPlot that it shows like the screenshot. It only shows the dot but no distribution of the data, is that normal?enter image description here

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    $\begingroup$ Hello Hua, welcome to bioinformatics.SE. If you search google images for "Vln Plot", you find how it should look like, for instance. We are happy to help with questions, but we kindly ask people to devote some effort in resolving problem by their own and showing the research effort in the question. Also note that we don't see your data, it's very hard to guess what is wrong with your plots without it. My guess is that you have vast vast majority of data points == 0. $\endgroup$ – Kamil S Jaron Aug 31 '18 at 20:03
  • $\begingroup$ But is it possible to show the distribution for lowly expressed genes? How can I manually set the parameters in vlnplot() function to show the contours? $\endgroup$ – Shanlin Tong Jan 7 at 11:01
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I assume you are referring to VlnPlot() of Seurat. The reason that you are getting such a plot is because your distribution is highly skewed, most of your points are zeros, not surprising for scRNA-seq. And the plot is actually showing your distributions, it is just the points at zero stacking on top of each other.

You can double check this by plotting a histogram for each of the clusters.

An example violin plot:

enter image description here

Cluster 0, which is mostly zeros, kind of looks like yours.

enter image description here

Cluster 6, which I believe is what you would expect to see, contains a lot of cells that express the gene and much less skewed, hence the shape denoting the density.

enter image description here

So what you are seeing is normal, your gene is not expressed/not detected is all.

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Try using ridgeplots instead of violin plots. Ridge plots will show you that bump at zero

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