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Try to improve efficiency #4

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13 changes: 3 additions & 10 deletions R/Normalization.R
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ LogNormalizeUsingAlternateAssay <- function(seuratObj, assayToNormalize, assayFo
}

ratios <- c()
normalizedMat <- Seurat::as.sparse(cbind(sapply(seq_len(length.out = ncells), function(i){
normalizedMat <- Seurat::as.sparse(apply(X = seq_len(length.out = ncells), MARGIN = margin, simplify = FALSE, FUN = function(i){
x <- toNormalize[, i]
sumX <- sum(x)
librarySize <- sumX + assayForLibrarySizeData[i]
Expand All @@ -56,18 +56,11 @@ LogNormalizeUsingAlternateAssay <- function(seuratObj, assayToNormalize, assayFo
xnorm <- log1p(x = x / librarySize * scale.factor)

return(xnorm)
})))
}))
colnames(normalizedMat) <- colnames(toNormalize)
rownames(normalizedMat) <- rownames(toNormalize)
end_time <- Sys.time()

if (all(is.null(rownames(normalizedMat))) || any(rownames(toNormalize) != rownames(normalizedMat))) {
stop('Row names not equal')
}

if (all(is.null(colnames(normalizedMat))) || any(colnames(toNormalize) != colnames(normalizedMat))) {
stop('Column names not equal')
}

if (.doDebugLogging()) {
logger::log_info('Normalization done')
}
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