Switch to logger.info()

Author: bbimber

singlecell/resources/chunks/MergeSeurat.R

@@ -3,7 +3,7 @@ doDiet <- exists('doDiet') && doDiet
 mergeBatch <- function(dat) {
     toMerge <- list()
     for (datasetId in names(dat)) {
-        message(paste0('Loading: ', datasetId))
+        logger::log_info(paste0('Loading: ', datasetId))
         if (doDiet) {
             toMerge[[datasetId]] <- Seurat::DietSeurat(readSeuratRDS(dat[[datasetId]]))
             gc()
@@ -36,40 +36,40 @@ if (length(seuratObjects) == 1) {
     numBatches <- ceiling(length(seuratObjects) / batchSize)
     mergedObjectFiles <- list()
     for (i in 1:numBatches) {
-        message(paste0('Merging batch ', i, ' of ', numBatches))
+        logger::log_info(paste0('Merging batch ', i, ' of ', numBatches))
         start <- 1 + (i-1)*batchSize
         end <- min(start+batchSize-1, length(seuratObjects))
-        message(paste0('processing: ', start, ' to ', end, ' of ', length(seuratObjects)))
+        logger::log_info(paste0('processing: ', start, ' to ', end, ' of ', length(seuratObjects)))
 
         fn <- paste0('mergeBatch.', i, '.rds')
         saveRDS(mergeBatch(seuratObjects[start:end]), file = fn)
         mergedObjectFiles[[i]] <- fn
 
-        print('mem used:')
-        print(pryr::mem_used())
+        logger::log_info('mem used:')
+        logger::log_info(pryr::mem_used())
         gc()
     }
 
-    print('Done with batches')
+    logger::log_info('Done with batches')
     if (length(mergedObjectFiles) == 1) {
         seuratObj <- readRDS(mergedObjectFiles[[1]])
         unlink(mergedObjectFiles[[1]])
     } else {
-        message('performing final merge')
+        logger::log_info('performing final merge')
         seuratObj <- readRDS(mergedObjectFiles[[1]])
         unlink(mergedObjectFiles[[1]])
 
         for (i in 2:length(mergedObjectFiles)) {
-            print(paste0('Merging final file ', i, ' of ', length(mergedObjectFiles)))
+            logger::log_info(paste0('Merging final file ', i, ' of ', length(mergedObjectFiles)))
             seuratObj <- merge(x = seuratObj, y = readRDS(mergedObjectFiles[[i]]), project = seuratObj@project.name)
             if (HasSplitLayers(seuratObj)) {
                 seuratObj <- MergeSplitLayers(seuratObj)
             }
 
             unlink(mergedObjectFiles[[i]])
 
-            print('mem used:')
-            print(pryr::mem_used())
+            logger::log_info(paste0('mem used after merge batch ' , i , ' of ', length(mergedObjectFiles)))
+            logger::log_info(pryr::mem_used())
             gc()
         }
     }