Merge pull request dpeerlab#8 from dpeerlab/MultiCoreTSNE

Replace bhtsne with MultiCoreTSNE
imahabub · May 2, 2019 · ae0bdc0 · ae0bdc0
2 parents 3ca67cd + bdffeab
commit ae0bdc0
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/setup.py b/setup.py
@@ -39,7 +39,8 @@
           'phenograph',
           'tables>=3.4.2',
           'Cython',
-          'bhtsne',
+          'cmake',
+          'MulticoreTSNE',
           'matplotlib>=2.2.2',
           'seaborn>=0.8.1',
           'tzlocal',

diff --git a/src/palantir/utils.py b/src/palantir/utils.py
@@ -1,6 +1,6 @@
 import pandas as pd
 import numpy as np
-import bhtsne
+from MulticoreTSNE import MulticoreTSNE as TSNE
 import phenograph
 
 from sklearn.decomposition import PCA
@@ -129,8 +129,7 @@ def run_tsne(data, n_dim=2, perplexity=150, **kwargs):
     :param n_dim: Number of dimensions for tSNE embedding
     :return: tSNE embedding of the data
     """
-    tsne = bhtsne.tsne(data.values.astype(float),
-                       dimensions=n_dim, perplexity=perplexity, **kwargs)
+    tsne = TSNE(n_components=n_dim, perplexity=perplexity, **kwargs).fit_transform(data.values)
     tsne = pd.DataFrame(tsne, index=data.index)
     tsne.columns = ['x', 'y']
     return tsne