Seurat: Violin plot hidden behind cells

[piepertc]

Hi Seurat team,

I am unable to see the actual distribution visualization in my violin plots as the data in front is just too dense. Do you have any advice on how to maybe make the data points smaller or just show a subset of them that match the distributions?

I appreciate your help!

(Violin plots attached)

[unknowledgeable1]

Use a dot size = 0

On Fri, May 3, 2019, 1:45 PM piepertc [e-mail] wrote:

Hi Seurat team,

I am unable to see the actual distribution visualization in my violin
plots as the data in front is just too dense. Do you have any advice on how
to maybe make the data points smaller or just show a subset of them that
match the distributions?

I appreciate your help!

(Violin plots attached)
[image: Screen Shot 2019-05-03 at 3 44 32 PM]
https://user-images.githubusercontent.com/49733959/57164655-68bbe600-6dba-11e9-8c63-c270c7bf315b.png

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[piepertc]

The only methods I can find that modify dot size don't seem to work in the VlnPlot function. I'm not super familiar with R and don't have a great intuition about how to accomplish this. Thanks for your help!

[rmenafra]

Assuming you are using Seurat3 then the option for the VlnPlot is to set pt.size = 0. This will hide completely the dots.
VlnPlot(object, features , pt.size = 0)

[piepertc]

That did the trick; thanks!