Error in `Add_Mito_Ribo_Seurat

[amv33576]

Good day,

This is my command:
I have a list with the ribosomal gene names: ribo_gene_list

class(ribo_gene_list)
[1] "character"

head(ribo_gene_list)
[1] "Avfl.Avfl000001G13960" "Avfl.Avfl000034G2247.dok7" "Avfl.Avfl000153G27357.fasn3" "Avfl.Avfl000218G1006" "Avfl.Avfl000296G113.po11"
[6] "Avfl.Avfl000335G14670.inx7"

seuratObj <- Add_Mito_Ribo_Seurat(seuratObj, ribo_features = ribo_gene_list, species = "other")

I am adding species = "other", because it is a butterfly species, no found in the available list.

I get this error:

Error in Add_Mito_Ribo_Seurat():
! No features or patterns provided for mito/ribo genes.
ℹ Please provide a default species name or pattern/features.
Run rlang::last_trace() to see where the error occurred.

rlang::last_trace()
<error/rlang_error>
Error in Add_Mito_Ribo_Seurat():
! No features or patterns provided for mito/ribo genes.
ℹ Please provide a default species name or pattern/features.

---

Backtrace:
▆

1. └─scCustomize::Add_Mito_Ribo_Seurat(seuratObj, ribo_features = ribo_gene_list, species = "other")
   Run rlang::last_trace(drop = FALSE) to see 2 hidden frames.

rlang::last_trace(drop = FALSE)
<error/rlang_error>
Error in Add_Mito_Ribo_Seurat():
! No features or patterns provided for mito/ribo genes.
ℹ Please provide a default species name or pattern/features.

---

Backtrace:
▆

1. └─scCustomize::Add_Mito_Ribo_Seurat(seuratObj, ribo_features = ribo_gene_list, species = "other")
2. └─cli::cli_abort(...)

3. └─rlang::abort(...)
   

I am using scCustomize 1.1.3 and Seurat 4.9.9.9067

Not sure what I am doing wrong. Could you please help me?

Best,

Anyi

[samuel-marsh]

Hi Anyi,

Thanks for posting issue. I’ll take look at it. If you don’t mind, could you update to the develop_V5 branch and let me know if you get the same error?

Thanks!
Sam

[amv33576]

Thank you!

I updated it (1.9.9.9027), and it still shows the same error.

test <- Add_Mito_Ribo_Seurat(seurat_object = seuratObj, species = "other", ribo_features = ribo_gene_list)
Error in Add_Mito_Ribo_Seurat():
! No features or patterns provided for mito/ribo genes.
ℹ Please provide a default species name or pattern/features.
Run rlang::last_trace() to see where the error occurred.
rlang::last_trace()
<error/rlang_error>
Error in Add_Mito_Ribo_Seurat():
! No features or patterns provided for mito/ribo genes.
ℹ Please provide a default species name or pattern/features.

---

Backtrace:
▆

1. └─scCustomize::Add_Mito_Ribo_Seurat(seurat_object = seuratObj, species = "other", ribo_features = ribo_gene_list)
   Run rlang::last_trace(drop = FALSE) to see 2 hidden frames.

rlang::last_trace(drop = FALSE)
<error/rlang_error>
Error in Add_Mito_Ribo_Seurat():
! No features or patterns provided for mito/ribo genes.
ℹ Please provide a default species name or pattern/features.

---

Backtrace:
▆

1. └─scCustomize::Add_Mito_Ribo_Seurat(seurat_object = seuratObj, species = "other", ribo_features = ribo_gene_list)
2. └─cli::cli_abort(...)

3. └─rlang::abort(...)
   

[samuel-marsh]

Hi Anyi,

I believe I have fixed the issue and fix is now live in v1.9.9.9029. If you are still receiving this error or another one after updating to newest dev version please let me know here and I will reopen the issue.

Thanks!
Sam