Merge pull request #7 from DongzeHE/master

update loadFry function
thelovelab · Jul 23, 2021 · 19124e4 · 19124e4
2 parents 30691a1 + f0d9445
commit 19124e4
Showing 1 changed file with 54 additions and 48 deletions.
diff --git a/R/loadFry.R b/R/loadFry.R
@@ -44,57 +44,63 @@
 #'
 
 loadFry <- function(fry.dir, which_counts = c('S', 'A'), verbose = FALSE) {
-
-  # read in metadata
-  meta_info <- fromJSON(file.path(fry.dir, "meta_info.json"))
-  ng <- meta_info$num_genes
-  usa_mode <- meta_info$usa_mode
-
-  if (usa_mode) {
-    if (length(which_counts) == 0) {
-      stop("Please at least provide one status in 'U' 'S' 'A' ")
+    # in alevin-fry 0.4.1, meta_info.json is changed to quant.json, so check both
+    # read in metadata
+    qfile <- file.path(fry.dir, "quant.json")
+    if (!file.exists(qfile)) {
+      qfile <- file.path(fry.dir, "meta_info.json")
     }
-    if (verbose) {
-      message("processing input in USA mode, will return ", paste(which_counts, collapse = '+'))
+
+    # read in metadata
+    meta_info <- fromJSON(file = qfile)
+    ng <- meta_info$num_genes
+    usa_mode <- meta_info$usa_mode
+
+    if (usa_mode) {
+      if (length(which_counts) == 0) {
+        stop("Please at least provide one status in 'U' 'S' 'A' ")
+      }
+      if (verbose) {
+        message("processing input in USA mode, will return ", paste(which_counts, collapse = '+'))
+      }
+    } else if (verbose) {
+      message("processing input in standard mode, will return spliced count")
     }
-  } else if (verbose) {
-    message("processing input in standard mode, will return spliced count")
-  }
-
-  # read in count matrix
-  af_raw <-  readMM(file = file.path(fry.dir, "alevin", "quants_mat.mtx"))
-  # if usa mode, each gene gets 3 rows, so the actual number of genes is ng/3
-  if (usa_mode) {
-    if (ng %% 3 != 0) {
-      stop("The number of quantified targets is not a multiple of 3")
+
+    # read in count matrix
+    af_raw <-  readMM(file = file.path(fry.dir, "alevin", "quants_mat.mtx"))
+    # if usa mode, each gene gets 3 rows, so the actual number of genes is ng/3
+    if (usa_mode) {
+      if (ng %% 3 != 0) {
+        stop("The number of quantified targets is not a multiple of 3")
+      }
+      ng <- as.integer(ng/3)
     }
-    ng <- as.integer(ng/3)
-  }
-
-  # read in gene name file and cell barcode file
-  afg <-  read.table(file.path(fry.dir, "alevin", "quants_mat_cols.txt"), 
-                  strip.white = TRUE, header = FALSE, nrows = ng, 
-                  col.names = c("gene_ids"), row.names = 1)
-  afc <-  read.table(file.path(fry.dir, "alevin", "quants_mat_rows.txt"), 
-                  strip.white = TRUE, header = FALSE,
-                  col.names = c("barcodes"), row.names = 1)
-
-  # if in usa_mode, sum up counts in different status according to which_counts
-  if (usa_mode) {
-    rd <- list("S" = seq(1, ng), "U" =  seq(ng + 1, 2 * ng),
-               "A" =  seq(2 * ng + 1, 3 * ng))
-    o <- af_raw[, rd[[which_counts[1]]], drop = FALSE]
-    for (wc in which_counts[-1]) {
-      o <- o + af_raw[, rd[[wc]], drop = FALSE]
+
+    # read in gene name file and cell barcode file
+    afg <-  read.table(file.path(fry.dir, "alevin", "quants_mat_cols.txt"), 
+                    strip.white = TRUE, header = FALSE, nrows = ng, 
+                    col.names = c("gene_ids"), row.names = 1)
+    afc <-  read.table(file.path(fry.dir, "alevin", "quants_mat_rows.txt"), 
+                    strip.white = TRUE, header = FALSE,
+                    col.names = c("barcodes"), row.names = 1)
+
+    # if in usa_mode, sum up counts in different status according to which_counts
+    if (usa_mode) {
+      rd <- list("S" = seq(1, ng), "U" =  seq(ng + 1, 2 * ng),
+                "A" =  seq(2 * ng + 1, 3 * ng))
+      o <- af_raw[, rd[[which_counts[1]]], drop = FALSE]
+      for (wc in which_counts[-1]) {
+        o <- o + af_raw[, rd[[wc]], drop = FALSE]
+      }
+    } else {
+      o <- af_raw
     }
-  } else {
-    o <- af_raw
-  }
 
-  # create SingleCellExperiment object
-  sce <-  SingleCellExperiment(list(counts = t(o)),
-                              colData = afc,
-                              rowData = afg
-  )
-  sce
+    # create SingleCellExperiment object
+    sce <-  SingleCellExperiment(list(counts = t(o)),
+                                colData = afc,
+                                rowData = afg
+    )
+    sce
 }