Merge pull request #6 from dpeerlab/issue-3

ManuSetty · web-flow · commit e1f60a6a0117 · 2019-05-03T10:29:30.000+05:30
Fix for issue 3
diff --git a/setup.py b/setup.py
@@ -1,4 +1,3 @@
-import os
 import sys
 import shutil
 from subprocess import call
@@ -23,7 +22,7 @@
 setup(name='harmony',
       version=__version__,  # read in from the exec of version.py; ignore error   
       description='Harmony is a unified framework for data visualization, analysis and interpretation of scRNA-seq data measured across discrete time points',
-      url='https://github.com/manusetty/harmony',
+      url='https://github.com/dpeerlab/harmony',
       author='Manu Setty',
       author_email='manu.talanki@gmail.com',
       package_dir={'': 'src'},
@@ -35,6 +34,6 @@
           'sklearn',
           'fa2',
           'matplotlib>=2.2.2',
-          'seaborn>=0.8.1'          
+          'seaborn>=0.8.1'
       ],
       )
diff --git a/src/harmony/utils.py b/src/harmony/utils.py
@@ -84,8 +84,8 @@ def hvg_genes(norm_df, no_genes=1000):
     with warnings.catch_warnings():
         warnings.simplefilter('ignore')
         disp_mad_bin = disp_grouped.apply(robust.mad)
-    df['dispersion_norm'] = np.abs((df['dispersion'].values - disp_median_bin[df['mean_bin']].values)) \
-        / disp_mad_bin[df['mean_bin']].values
+    df['dispersion_norm'] = np.abs((df['dispersion'].values - disp_median_bin[df['mean_bin'].values].values)) \
+        / disp_mad_bin[df['mean_bin'].values].values
 
     # Subset of genes
     use_genes = df['dispersion_norm'].sort_values().index[::-1][:no_genes]
@@ -102,7 +102,7 @@ def run_pca(data, n_components=300, var_explained=0.85):
     number of components = min(n_components, components explaining var_explained)
     :return: PCA projections of the data and the explained variance
     """
-    init_components = min([n_components, data.shape[1]])
+    init_components = min([n_components, data.shape[0]])
     pca = PCA(n_components=init_components, svd_solver='randomized')
     pca.fit(data)
     if pca.explained_variance_ratio_.sum() >= 0.85:
diff --git a/src/harmony/version.py b/src/harmony/version.py
@@ -1 +1 @@
-__version__ = "0.1"
+__version__ = "0.1.1"

Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-__version__ = "0.1"`
	`1`	`+__version__ = "0.1.1"`