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ncborcherding / scRepertoire

A toolkit for single-cell immune profiling
https://www.borch.dev/uploads/screpertoire/
MIT License
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percentVJ all 0 #415

Closed jiw181 closed 1 month ago

jiw181 commented 1 month ago

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 commented 1 month ago

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 commented 1 month ago

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 commented 1 month ago

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 commented 1 month ago

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 GitHubhttps://github.com/ncborcherding/scRepertoire/issues/415#issuecomment-2400726373, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AXFDRPLDJKTCKLZL26C4523Z2Q3P3AVCNFSM6AAAAABPS4N6PSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMBQG4ZDMMZXGM. You are receiving this because you were mentioned.Message ID: @.***>