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ncborcherding / scRepertoire

A toolkit for single-cell immune profiling
https://www.borch.dev/uploads/screpertoire/
MIT License
311 stars 54 forks source link

getCirclize - custom variable Bug #418

Closed jakob-arnold closed 1 month ago

jakob-arnold commented 1 month ago

Hi,

Thank you so much for the great package!

I want to use the getCirclize() function and use a custom variable for the cloneCallargument. I noticed a bug in this function

When I try running the following code chord.df <- getCirclize(gd, cloneCall="TRD_strict", group.by = "cluster", proportion=F)

I get an error Warning in .convertClonecall(x) : A custom variable trd_strict will be used to call clones Error in .theCall(meta, cloneCall) : Check the clonal variable (cloneCall) being used in the function, it does not appear in the data provided.

I noticed, that in the error it says "A custom variable trd_strict will be used to call clones". When I change the variable to be all lower case letters, it works. I guess, there is an issue with letter casing?

Also on a side note: In the documentation, the include.self argument is mentioned. However, it seems like that argument is not implemented yet, right?

Error in getCirclize(gd, cloneCall = "TRD_strict", group.by = "cluster", : unused argument (include.self = T)

Best Jakob

ncborcherding commented 1 month ago

Hey Jakob,

Should be fixed from this issue: #405

Try installing the current main branch with: devtools::install_github("ncborcherding/scRepertoire")

This might also solve the include.self issue, as that is in the current version on the main repo

Hope that helps and let me know if the problem persists - make sure to restart your R session after updating.

Thanks, Nick