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AllenInstitute / scrattch.mapping

Genearlized mapping scripts for RNA-seq and Patch-seq data
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taxonomyName input to loadTaxonomy not working as expected #24

Closed scseeman closed 1 year ago

scseeman commented 1 year ago

I tried using the new taxonomyName input to loadTaxonomy and I can't get it to work. Maybe I'm not using it properly but I looked at the code to see what the format should be.

Code:

taxonomy_path  =  "//allen/programs/celltypes/workgroups/rnaseqanalysis/shiny/10x_seq/NHP_BG_AIT_115/"
loadTaxonomy(refFolder = taxonomy_path, taxonomyName = "NHP_BG_AIT115_taxonomy")

Error:

Error in loadTaxonomy(refFolder = taxonomy_path, taxonomyName = "NHP_BG_AIT115_taxonomy") : 
  unused argument (taxonomyName = "NHP_BG_AIT115_taxonomy")
Execution halted

I am running latest on the singularity singularity exec --cleanenv docker://bicore/scrattch_mapping:latest Rscript scrattch_mapping.R

scseeman commented 1 year ago

nevermind, I see this is suppose to be used with buildTaxonomy not loadTaxonomy. Though that would be a nice feature to be able to specify a particular h5ad file in the load

leechangkyu commented 1 year ago

The function loadTaxonomy() expects the following inputs loadTaxonomy = function(taxonomyDir, sample_id = "sample_id", hGenes=NULL, gene_id = "gene", force=FALSE)

Try loadTaxonomy("//allen/programs/celltypes/workgroups/rnaseqanalysis/shiny/10x_seq/NHP_BG_AIT_115/NHP_BG_AIT115_taxonomy")

From: Stephanie Seeman @.> Sent: Monday, June 05, 2023 10:30 AM To: AllenInstitute/scrattch-mapping @.> Cc: Subscribed @.***> Subject: [AllenInstitute/scrattch-mapping] taxonomyName input to loadTaxonomy not working as expected (Issue #24)

I tried using the new taxonomyName input to loadTaxonomy and I can't get it to work. Maybe I'm not using it properly but I looked at the code to see what the format should be.

Code:

taxonomy_path = "//allen/programs/celltypes/workgroups/rnaseqanalysis/shiny/10x_seq/NHP_BG_AIT_115/"

loadTaxonomy(refFolder = taxonomy_path, taxonomyName = "NHP_BG_AIT115_taxonomy")

Error:

Error in loadTaxonomy(refFolder = taxonomy_path, taxonomyName = "NHP_BG_AIT115_taxonomy") :

unused argument (taxonomyName = "NHP_BG_AIT115_taxonomy")

Execution halted

I am running latest on the singularity singularity exec --cleanenv docker://bicore/scrattch_mapping:latest Rscript scrattch_mapping.R

- Reply to this email directly, view it on GitHubhttps://github.com/AllenInstitute/scrattch-mapping/issues/24, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEXNJFQ4GURIEDZA6VT5S4TXJYJSXANCNFSM6AAAAAAY3I54AY. You are receiving this because you are subscribed to this thread.Message ID: @.**@.>>