related to djvdj library

[Rimanpreet1]

I tried to use djvdj library to merge vdj data in seurat object, everytime it gave this error "Error in import_vdj(): ! The provided cell prefixes (vdjt_) do not match those in the input object ()

Backtrace: ▆

1. └─djvdj::import_vdj(so, vdj_dir = vdj_dirs, prefix = "")
2. └─cli::cli_abort("The provided cell prefixes ({vdj_prfxs}) do not match\n those in the input object ({prfxs})")
3. └─rlang::abort(...)" could you please help me to fix this

[sheridar]

Hi @Rimanpreet1, can you send the command you're running that produces this error

[Rimanpreet1]

paths <- here("vdj_t") so_avid<- import_vdj( input = so, vdj_dir = paths, filter_chains = TRUE, filter_paired = FALSE )

But now, it is showing, "plot_clonal_abundace" function is not available in djvdj library, Here is the code "so_avid <- calc_frequency(input = so_avid, cluster_col = "seurat_clusters", data_col = "clonotype_id")

@.**@.>)

plot_clonal_abundance( input = so_avid, cluster_col = "seurat_clusters", n_clones = 10, type = "bar", ) "

Regards, Rimanpreet From: Ryan Sheridan @.> Sent: Sunday, August 20, 2023 9:17 PM To: rnabioco/djvdj @.> Cc: Kaur, Rimanpreet @.>; Mention @.> Subject: Re: [rnabioco/djvdj] related to djvdj library (Issue #135)

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Hi @Rimanpreet1https://github.com/Rimanpreet1, can you send the command you're running that produces this error

- Reply to this email directly, view it on GitHubhttps://github.com/rnabioco/djvdj/issues/135#issuecomment-1685478053, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BCBATKLLDN67LVPFXQPMQMLXWKZJLANCNFSM6AAAAAA3XL4IQY. You are receiving this because you were mentioned.Message ID: @.**@.>>

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[Rimanpreet1]

now, no one function is available in djvdj library, every time I run it showed, could not find function

[sheridar]

Are you loading the package using library(djvdj)? It should also be noted that the package is under active development and the functionality is subject to change. The plot_clonal_abundance() function has been replaced with plot_clone_frequency() in the most recent version available on github.

If you have recently installed the package, I would recommend trying the vignettes listed under "Articles" on our github page for the most up-to-date information.

Are you still encountering the initial error about the cell prefixes not matching? This is essentially saying that the cell barcodes for your VDJ data do not match the cell barcodes in your Seurat object.

Can you send me your "filtered_contig_annotations.csv" file, located in the "outs" directory for the cellranger run. I can take a look at this to see if there are any obvious issues.

[sheridar]

I am going to close this issue, please open a new issue if you have any other issues or questions about the package