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extracting input files form Seurat

Hi,

I am using codes pasted below to obtain Volcano plots, dot plots, feature plot etc for the single cell data analysis by using commands pasted below:

VlnPlot(Seurat_object, features = "X", group.by = "Names",split.by= "condition", slot="data")
DotPlot(Seurat_object, features ="X") + RotatedAxis()
RidgePlot(Seurat_object, features = "X", assay = "RNA", group.by = "condition",slot="data")
FeaturePlot(Seurat_object, features = "X", slot="data", split.by= "condition",label=TRUE)

I wanted to learn how to extract the input files Seurat uses to generate these figures?

Thank you

Best,
R

seurat single-cell
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written by rasing02 • rasing02

Just to be clear, you want to export the (input) data used for plots into actual files?

• 0 views • link
written by GenoMax GenoMax

Yes, I just need the input data so that investigators can use tools other than R to visualize the data in form of viloin plots or feature plots or dot plots or box plots etc

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written by rasing02 • rasing02

1 answer

You can get the data behind any of the plots easily enough:

p <- VlnPlot(Seurat_object, features = "X", group.by = "Names",split.by= "condition", slot="data")
p$data # Contains all the info used in the plot.
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written by jared.andrews07 jared.andrews07

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