small changes, rerun notebooks

volkamerlab · Feb 3, 2025 · 8714ca9 · 8714ca9
1 parent b1cf797
commit 8714ca9
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Showing 10 changed files with 356 additions and 465 deletions.
diff --git a/kinfraglib/filters/plots.py b/kinfraglib/filters/plots.py
@@ -331,7 +331,7 @@ def sample_subset(fragment_library, sample):
     return fragment_library_subset
 
 
-def create_tsne_embeddings(fragment_library):
+def create_tsne_embeddings(fragment_library, n_components):
     """
     Creates the t-SNE embedding for all following t-SNE plots
     ----------
@@ -345,7 +345,7 @@ def create_tsne_embeddings(fragment_library):
         MACCSkeys.GenMACCSKeys
     )
 
-    pca = PCA(n_components=30)
+    pca = PCA(n_components)
     crds = pca.fit_transform(list(fragment_library_concat["maccs"]))
 
     crds_embedded = TSNE(

diff --git a/notebooks/custom_kinfraglib/2_2_custom_filters_analysis.ipynb b/notebooks/custom_kinfraglib/2_2_custom_filters_analysis.ipynb
diff --git a/notebooks/custom_kinfraglib/2_3_custom_filters_paper.ipynb b/notebooks/custom_kinfraglib/2_3_custom_filters_paper.ipynb
diff --git a/notebooks/custom_kinfraglib/figures/tsne_bool_bb.png b/notebooks/custom_kinfraglib/figures/tsne_bool_bb.png
diff --git a/notebooks/custom_kinfraglib/figures/tsne_bool_brenk.png b/notebooks/custom_kinfraglib/figures/tsne_bool_brenk.png
diff --git a/notebooks/custom_kinfraglib/figures/tsne_bool_custom.png b/notebooks/custom_kinfraglib/figures/tsne_bool_custom.png
diff --git a/notebooks/custom_kinfraglib/figures/tsne_bool_pains.png b/notebooks/custom_kinfraglib/figures/tsne_bool_pains.png
diff --git a/notebooks/custom_kinfraglib/figures/tsne_bool_qed.png b/notebooks/custom_kinfraglib/figures/tsne_bool_qed.png
diff --git a/notebooks/custom_kinfraglib/figures/tsne_bool_ro3.png b/notebooks/custom_kinfraglib/figures/tsne_bool_ro3.png
diff --git a/notebooks/custom_kinfraglib/figures/tsne_bool_syba.png b/notebooks/custom_kinfraglib/figures/tsne_bool_syba.png