Cells without alpha chain

[nicoac]

Hello! Really enjoying the package. I have a question regarding cells without alpha chains and how they should be interpreted. I have a very large TCR clonotype that is returning without an alpha chain and I'm having a hard time understanding why this would be the case based on the qc steps that were taken.

Results of QC:

Clonotype network after ct_cluster_aa_alignment

Any advice or thoughts would be much appreciated!

[grst]

Hi @nicoac,

how did you do the QC filtering?
Because from your figure, this is totally expected - "Orphan VDJ" refers to cells having a beta chain only.

[nicoac]

Now that you've said that I realized I'm not dumping out the orphan VDJ, only the multi-chain. Is it possible to filter those cells as the multi-chain was done here? : adata = adata[adata.obs["multi_chain"] != "True", :].copy().

I guess I'm just surprised with how large that clone appears in the clonotype network graph when looking at the bar graph.

[grst]

Sure! You can always check the available categories of a column in obs with

adata.obs['chain_pairing'].unique()

To filter, you can use, e.g.

adata = adata[~adata.obs["chain_pairing"].isin(["orphan VDJ", "orphan VJ", "no IR"]), :].copy()

(untested, hope there are no typos)

[grst]

Closing this for now - feel free to reopen if there are any other questions!

[nicoac]

Thanks so much Gregor. Will try this out soon.