Analyzing TCR clonotype in Seurat

Question

[roberts]

Hello, I have merged my VDJ data into my Seurat object by adding it as metadata. Now is there a way to for example pull out of the CD8 TCR data and look at those clonotypes vs. CD4 TCR. How would you go about looking at different clonotypes in Seurat. Thank you!

[rpolicastro]

I can't give any specific advice because of how broad the question is, but many plotting and analysis functions will have group.by and split.by arguments that let you work with different columns in your meta-data. You can also use the subset function to return a seurat object that contains only cells matching your logical condition, such as clonotype.

Answer 1

[jared.andrews07]

This is complicated by there likely being thousands or hundreds of clonotypes in your data. How exactly do you want to visualize them? You may want to give the scRepertoire package a shot, it has a fair number of good visualizations, particularly for clonal analyses.