default tsne

volkamerlab · Nov 12, 2024 · d84df6e · d84df6e
1 parent fe806fb
commit d84df6e
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Showing 2 changed files with 14 additions and 4 deletions.
diff --git a/kinfraglib/filters/plots.py b/kinfraglib/filters/plots.py
@@ -332,9 +332,18 @@ def debug_tsne(fragment_library):
     pca = PCA(n_components=50)
     crds = pca.fit_transform(list(fragment_library_concat["maccs"]))
 
-    # crds_embedded = TSNE(
-    #    n_components=2, init="pca", learning_rate="auto"
-    # ).fit_transform(crds)
+    crds_embedded = TSNE(
+        n_components=2, init="pca", learning_rate="auto"
+    ).fit_transform(crds)
+
+
+def debug_tsne_v2():
+    import numpy as np
+
+    X = np.array([[0, 0, 0], [0, 1, 1], [1, 0, 1], [1, 1, 1]])
+    X_embedded = TSNE(
+        n_components=2, learning_rate="auto", init="random", perplexity=3
+    ).fit_transform(X)
 
 
 def create_tsne_plots(fragment_library):

diff --git a/notebooks/custom_kinfraglib/2_2_custom_filters_analysis.ipynb b/notebooks/custom_kinfraglib/2_2_custom_filters_analysis.ipynb
@@ -1142,7 +1142,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "filters.plots.debug_tsne(fragment_library)"
+    "#filters.plots.debug_tsne(fragment_library)\n",
+    "filters.plots.debug_tsne_v2()"
    ]
   },
   {