percentVJ all 0

[jiw181]

Hello,

For the percentVJ function, I got all 0 in the output for 2 of the samples. However, I am sure the V and J are present for the 2 samples in the Seurat object as shown in the attached file.
unknown_error.xlsx

If I only run the 2 samples, I got error: Error in combine_vars():
! Faceting variables must have at least one value

If I only run 1 sample, I got error:
Error in View : 'names' attribute [1] must be the same length as the vector [0]

Any suggestions?

Many thanks

[ncborcherding]

Hey @jiw181,

Thanks for reaching out.

Please make a reproducible example for this issue so I know what you are experiencing.

Also with the example, please make sure to include the output of sessionInfo()

Thanks,
Nick

[jiw181]

Hello Nick @ncborcherding,

Thank you for the prompt response! Please find the .html with sessionInfo and intermediate files attached.
rstudio-export (47).zip

Thank you!

[ncborcherding]

Found the issue - there was an assumption that there would be more than 1 sample during the plotting phase. It looks like subseting it to one specific orig.ident was what was causing it to break.

Got it fixed and in the dev branch. I will need to do some more testing this week and get it merged to the main branch.

For now, you can install the dev branch with:

devtools::install_github("ncborcherding/scRepertoire@dev")

Thanks,
Nick

[jiw181]

I will test the dev version and see if it reports correct pct for the 2 samples. Thank you very much. Have a great day! 😊 From: theHumanBorch ***@***.***> Date: Tuesday, October 8, 2024 at 4:07 PM To: ncborcherding/scRepertoire ***@***.***> Cc: Wang, Jiefei ***@***.***>, Mention ***@***.***> Subject: Re: [ncborcherding/scRepertoire] percentVJ all 0 (Issue #415) Found the issue - there was an assumption that there would be more than 1 sample during the plotting phase. It looks like subseting it to one specific orig.ident was what was causing it to break. Got it fixed and in the dev branch. I will need to do some more testing this week and get it merged to the main branch. For now, you can install the dev branch with: ***@***.***") Thanks, Nick — Reply to this email directly, view it on GitHub<#415 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AXFDRPLDJKTCKLZL26C4523Z2Q3P3AVCNFSM6AAAAABPS4N6PSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMBQG4ZDMMZXGM>. You are receiving this because you were mentioned.Message ID: ***@***.***>