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feat: pre flight safety checks #9

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feat: pre flight safety checks #9

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17 changes: 17 additions & 0 deletions R/makeShinyFilesGEX.R
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Original file line number Diff line number Diff line change
Expand Up @@ -135,6 +135,23 @@ makeShinyFilesGEX <- function(
}
sc1conf$ID = as.character(sc1conf$ID) # Remove levels

# Filter sc1meta to only cells present in all dimension reductions.
# A mismatch occurs when the Seurat object contains cells in @meta.data that
# are absent from @reductions (e.g. after reference-based mapping or merging).
# Indexing a matrix with an unknown rowname throws "subscript out of bounds".
if(class(obj)[1] == "Seurat"){
for(iDR in dimred.to.use){
drCells = rownames(obj@reductions[[iDR]]@cell.embeddings)
nBefore = nrow(sc1meta)
sc1meta = sc1meta[cellID %in% drCells]
nDropped = nBefore - nrow(sc1meta)
if(nDropped > 0){
warning(paste0(nDropped, " cell(s) in metadata have no embeddings in '",
iDR, "' and were dropped from the Shiny app."))
}
}
}

# Make prefix_dimr.rds
sc1dimr = list()
if(class(obj)[1] == "Seurat"){
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