Expression plots of some genes of interest from scRNA data for each library

Question

[entropy]

I am new to scRNA analysis and confused on a simple problem.

I have some genes of interest and I want to see their expression levels by plotting them over each library. My data is a 10X Genomics 3’ single cell RNA seq dataset. It has three libraries and they were normalized together. When I look at the barcdoe.tsv file of it, I see this kind of entries: AACCTGAGCCAATT-1

When I processed this data and get the unique values of the numbers after dash (-) symbol, I got (1,2,3) and it seems each refer to one of the of the three libraries.

How can I plot expressions of my genes per library? I used this tutorial https://satijalab.org/seurat/v3.0/pbmc3k_tutorial.html but VlnPlot does not seem to provide me what I want.

Thanks

[Arup Ghosh]

Try using library id as the Idents in the combined Seurat object.

[entropy]

I tried but it seems Idents is for the clusters but not each of the three libraries. Do you have any idea on how can I use it to get expressions for each of the three libraries.

[shoujun.gu]

You can always do it manually. For violin plot, its pretty straight forward: 1). export you data to a new dataframe, with columns of ['expression_of _interested_gene', 'library_id']; 2) plot the violin plot.

But if you want to plot the expression of a certain gene from a specific library on the original umap/tsne figure, you need to understand the data structure of seurat object, since you need the coordinates information.

Answer 1

[entropy]

I ended up doing this manually.