Disable unit variance scalling. Filter low expressed genes/transcript…

…s >0 instead of >1. (#10)
zavolanlab · Oct 15, 2020 · 547a106 · 547a106
1 parent 39a08a7
commit 547a106
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/scripts/zpca-tpm b/scripts/zpca-tpm
@@ -37,8 +37,8 @@ def main():
     parser.add_argument(
         "--tpm-filter",
         dest="tpm_filter",
-        default=1,
-        help="Filter genes/transcripts with mean expression less than the provided filter. Default: 1",
+        default=0,
+        help="Filter genes/transcripts with mean expression less than the provided filter. Default: 0",
         required=False,
     )
 

diff --git a/setup.py b/setup.py
@@ -13,7 +13,7 @@
 
 setup(
     name='zpca',
-    version='0.5',
+    version='0.7',
     description="PCA analysis for genes or transcripts.",
     author="Foivos Gypas",
     author_email='[email protected]',

diff --git a/zpca/zpca.py b/zpca/zpca.py
@@ -28,7 +28,7 @@ def perform_pca(df, n_components):
 
     df = df.astype(float)
 
-    scaled_data = preprocessing.scale(df.T)
+    scaled_data = preprocessing.scale(df, with_std=False)
 
     pca = PCA(n_components=n_components)
     pca.fit(scaled_data)