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Try to improve performance of NimbleAppend #2

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Merged
bbimber merged 1 commit into from
Mar 28, 2026
Merged

Try to improve performance of NimbleAppend #2

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21 changes: 14 additions & 7 deletions R/NimbleAppend.R
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Original file line number Diff line number Diff line change
Expand Up @@ -204,13 +204,6 @@ AppendNimbleCounts <- function(seuratObj, nimbleFile, targetAssayName, maxAmbigu

appendToExistingAssay <- targetAssayName %in% names(seuratObj@assays)

# Fill zeroed barcodes that are in seurat but not in nimble
zeroedBarcodes <- setdiff(colnames(seuratObj), colnames(df)[-1])
print(paste0('Total cells lacking nimble data: ', length(zeroedBarcodes), ' of ', ncol(seuratObj), ' cells'))
for (barcode in zeroedBarcodes) {
df[barcode] <- 0
}

# Cast nimble df to matrix
if (debugLogging) {
logger::log_info('Casting to a sparse matrix')
Expand All @@ -228,6 +221,20 @@ AppendNimbleCounts <- function(seuratObj, nimbleFile, targetAssayName, maxAmbigu
stop(paste0('Error: no column names in nimble count matrix, size: ', paste0(dim(m), collapse = ' by ')))
}

# Fill zeroed barcodes that are in seurat but not in nimble
zeroedBarcodes <- setdiff(colnames(seuratObj), colnames(m))
print(paste0('Total cells lacking nimble data: ', length(zeroedBarcodes), ' of ', ncol(seuratObj), ' cells'))
if (length(zeroedBarcodes) > 0) {
if (debugLogging) {
logger::log_info('Adding zeros for missing barcodes')
}

toAdd <- matrix(rep(0, length(zeroedBarcodes)*nrow(m)), ncol = length(zeroedBarcodes))
dimnames(toAdd) <- list(featureNames, zeroedBarcodes)
toAdd <- Seurat::as.sparse(toAdd)
m <- cbind(m, toAdd)
}

m <- m[,colnames(seuratObj), drop=FALSE] # Ensure column order matches
if (appendToExistingAssay && ncol(m) != ncol(seuratObj@assays[[targetAssayName]])) {
stop(paste0('Error parsing nimble data, ncol not equal after subset, was ', ncol(m)))
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