I have followed the Seurat Tutorial:Integrating stimulated vs. control PBMC datasets to learn cell-type specific responses by using my data. And I am confused about how to write the script to calculate the cell number of each sample on each cluster.

I have run TSENPlot to know the samples and I'm using another TSENPlot to get the clusters. If I want to know find the cluster1 of each sample's number how can I write the script?

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  • 1
    $\begingroup$ Please edit your question and give us some more details. What exactly do you need? Can you show us the code you have run? $\endgroup$
    – terdon
    Mar 5, 2019 at 10:22

1 Answer 1


Assuming you are following the basic seurat guide:


You can access the 'ident' slot of your Seurat object and you will get a vector of the cluster IDs and the names will be the respective cells.

Cell1A7 Cell1C4 Cell1D1 Cell1D2 Cell1D3 Cell1D5
0 3 3 1 3 1 
Levels: 0 1 2 3 4
  • $\begingroup$ In my example, the printing wasn't great but essentially Cell1A7 is in cluster 0, Cell 1C4 is in cluster 3, etc... $\endgroup$
    – story
    Mar 5, 2019 at 10:09

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