Merge pull request #64 from brianhie/no_tsne

Remove custom t-SNE implementation
brianhie · May 3, 2020 · 485b3a6 · 485b3a6
2 parents fdd1232 + 31a1ba0
commit 485b3a6
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Showing 4 changed files with 8 additions and 894 deletions.
diff --git a/scanorama/__init__.py b/scanorama/__init__.py
@@ -1,3 +1,3 @@
 from .scanorama import *
 
-__version__ = '1.5.2'
+__version__ = '1.6'
diff --git a/scanorama/scanorama.py b/scanorama/scanorama.py
@@ -13,7 +13,6 @@
 import sys
 import warnings
 
-from .t_sne_approx import TSNEApprox
 from .utils import plt, dispersion, reduce_dimensionality
 from .utils import visualize_cluster, visualize_expr, visualize_dropout
 from .utils import handle_zeros_in_scale
@@ -421,14 +420,15 @@ def visualize(assembled, labels, namespace, data_names,
               n_iter=N_ITER, perplexity=PERPLEXITY, verbose=VERBOSE,
               learn_rate=200., early_exag=12., embedding=None,
               shuffle_ds=False, size=1, multicore_tsne=True,
-              image_suffix='.svg', viz_cluster=False, colors=None):
+              image_suffix='.svg', viz_cluster=False, colors=None,
+              random_state=None,):
     # Fit t-SNE.
     if embedding is None:
         try:
             from MulticoreTSNE import MulticoreTSNE
             tsne = MulticoreTSNE(
                 n_iter=n_iter, perplexity=perplexity,
-                verbose=verbose, random_state=69,
+                verbose=verbose, random_state=random_state,
                 learning_rate=learn_rate,
                 early_exaggeration=early_exag,
                 n_jobs=40
@@ -437,9 +437,9 @@ def visualize(assembled, labels, namespace, data_names,
             multicore_tsne = False
 
         if not multicore_tsne:
-            tsne = TSNEApprox(
+            tsne = TSNE(
                 n_iter=n_iter, perplexity=perplexity,
-                verbose=verbose, random_state=69,
+                verbose=verbose, random_state=random_state,
                 learning_rate=learn_rate,
                 early_exaggeration=early_exag
             )