From ff3178eebd7e395d0bba5bbd8c3c67b9010ff47f Mon Sep 17 00:00:00 2001
From: mase5 <maxime.dewaegeneer@kuleuven.be>
Date: Wed, 5 Dec 2018 17:05:43 +0100
Subject: [PATCH] Fix bug when using build_loom with sparse matrices (e.g.:
 dgCMatrix).

---
 DESCRIPTION |  4 ++--
 R/loom.R    | 20 +++++++++++++++-----
 README.md   |  5 ++++-
 3 files changed, 21 insertions(+), 8 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 42b6ad7..b775158 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,13 +1,13 @@
 Package: SCopeLoomR
 Type: Package
 Title: Build .loom files (compatible with SCope) and extract data from .loom files.
-Version: 0.3.0
+Version: 0.3.1
 Author: mase5
 Maintainer: mase5 <mdewaegeneer@gmail.com>
 Description: R package to build generic .loom files aligning with the default naming convention of the .loom format and 
     to integrate other data types e.g.: regulons (SCENIC), clusters from Seurat, ... The package can also be used to extract
     data from .loom files.
-Imports: hdf5r, rjson, utils, methods, base, base64enc, igraph, plyr, rlist
+Imports: hdf5r, rjson, utils, methods, base, base64enc, igraph, plyr, rlist, Matrix
 Suggests: seurat, stringr
 License: Apache-2
 Encoding: UTF-8
diff --git a/R/loom.R b/R/loom.R
index f98d4d7..6939aa2 100644
--- a/R/loom.R
+++ b/R/loom.R
@@ -1162,6 +1162,7 @@ build_loom<-function(file.name
                      , fbgn.gn.mapping.file.path = NULL
                      , chunk.size = 1000
                      , display.progress = T) {
+  is.dgem.sparse<-F
   loom<-H5File$new(filename = file.name, mode = "w")
   tryCatch({
     print("Adding global attributes...")
@@ -1193,9 +1194,10 @@ build_loom<-function(file.name
     if(class(dgem) == "dgTMatrix") {
       print("Converting to dgCMatrix...")
       dgem<-methods::as(object = dgem, Class = "dgCMatrix")
-    } else if(class(dgem) == "dgTMatrix") {
-      print("Converting to Matrix...")
-      dgem<-as.matrix(x = dgem)
+    }
+    # Check if sparse matrix
+    if(sum(class(x = dgem) %in% c("dgCMatrix","dgTMatrix")) > 0) {
+      is.dgem.sparse<-T
     }
     print("Adding matrix...")
     add_matrix(loom = loom, dgem = dgem, chunk.size = chunk.size, display.progress = display.progress)
@@ -1206,13 +1208,21 @@ build_loom<-function(file.name
     # Check if matrix is raw counts
     if(sum(dgem%%1!=0) == 0) {
       print("Adding default metrics nUMI...")
-      nUMI<-colSums(dgem)
+      if(is.dgem.sparse) {
+        nUMI<-Matrix::colSums(dgem)
+      } else {
+        nUMI<-colSums(dgem)
+      }
       add_col_attr(loom = loom, key = "nUMI", value = nUMI, as.metric = T)
     } else {
       warning("Default metric nUMI was not added because the input matrix does not seem to be the raw counts.")
     }
     print("Adding default metrics nGene...")
-    nGene<-colSums(dgem > 0)
+    if(is.dgem.sparse) {
+      nGene<-Matrix::colSums(dgem > 0)
+    } else {
+      nGene<-colSums(dgem > 0)
+    }
     add_col_attr(loom = loom, key = "nGene", value = nGene, as.metric = T)
     print("Adding default embedding...")
     # Add the default embedding
diff --git a/README.md b/README.md
index fba8901..cecbe67 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# SCopeLoomR v0.3.0
+# SCopeLoomR v0.3.1
 An R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ... The package can also be used to extract
 data from .loom files.
 
@@ -36,6 +36,9 @@ You can find a tutorial on how to create .loom files and extract data from them
 
 November 8, 2018
 
+* Version 0.3.1
+    * Fix bug when adding sparse matrices.
+
 * Version 0.3.0
     * Add feature to extract the gene expression matrix of a given cluster.
     * Update [tutorial](https://github.com/aertslab/SCopeLoomR/blob/master/vignettes/SCopeLoomR_tutorial.Rmd).