Add cellassign organs to metadata #608
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jashapiro
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Dec 7, 2023
Co-authored-by: Joshua Shapiro <[email protected]>
allyhawkins
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Dec 7, 2023
| @@ -216,6 +226,17 @@ if (!is.null(opt$cellassign_predictions)) { | |||
| # note that if `metadata(sce)$celltype_methods` doesn't exist yet, this will | |||
| # come out to just the string "cellassign" | |||
| metadata(sce)$celltype_methods <- c(metadata(sce)$celltype_methods, "cellassign") | |||
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| # add cellassign reference organs to metadata | |||
| cellassign_organs <- opt$celltype_ref_metafile |> | |||
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I say we just keep it at organs to keep it consistent with how PanglaoDB (and we) refer to them.
Co-authored-by: Ally Hawkins <[email protected]>
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…organ-description Add cellassign organs to metadata
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Part of #589
This is the first of two PRs to get cellassign organs/tissues into the cell type report. Here, I just modify the
add_celltypes_to_sceprocess and associated R script to get info into the metadata. Since we only need to do this for cellassign references, I set up nextflow to only pass in the file to R if cellassign is present.Screen shot of resulting
metadata(sce)-While I was there, I also added in some file checks for cell typing files, which seemed like it couldn't hurt! One question is should we call these
organsortissues? I went with organs since that's what we already call them. Also, my checks for whether we grabbed the organs successfully are maybe overkill, any thoughts?FYI I opened a related docs issue as well - AlexsLemonade/scpca-docs#211
*Edit - the next PR will get this into the cell type report!
Probably the main report cell type section so it appears in both htmls.*edit 2: nope, we refer folks to the supplemental report for this sort of information!