Merge pull request #41 from KrishnaswamyLab/dev

Fix EB tutorial memory issue
KrishnaswamyLab · Jun 27, 2018 · 946a4ae · 946a4ae
2 parents d524144 + 39bc484
commit 946a4ae
Showing 1 changed file with 6 additions and 3 deletions.
diff --git a/Python/tutorial/EmbryoidBody.ipynb b/Python/tutorial/EmbryoidBody.ipynb
@@ -281,9 +281,12 @@
    "source": [
     "mito_genes = [gene_symbol.startswith('MT-') for gene_symbol in EBT_counts.columns] # Get all mitochondrial genes. There are 14, FYI.\n",
     "\n",
-    "lib_size =  EBT_counts.sum(axis=1)\n",
+    "lib_size = EBT_counts.to_coo().tocsr().sum(axis=1)\n",
     "\n",
-    "mito_expression = np.mean(EBT_counts.loc[:,mito_genes].values / lib_size.values[:,None], axis=1)\n",
+    "mito_expression = (EBT_counts.loc[:,mito_genes].to_coo().tocsr().multiply(1 / lib_size)).mean(axis=1)\n",
+    "\n",
+    "mito_expression = np.array(mito_expression).flatten() # mean returns a matrix, we want an array\n",
+    "lib_size        = np.array(lib_size).flatten()\n",
     "\n",
     "top_pct = np.percentile(mito_expression, 90) # top 10 percentile"
    ]
@@ -386,7 +389,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "genes_keep = np.sum(EBT_counts > 0, axis=0) > 10\n",
+    "genes_keep = (EBT_counts > 0).sum(axis=0) > 10\n",
     "EBT_counts = EBT_counts.loc[:,genes_keep]"
    ]
   },