Updated examples.

ArianeMora · Dec 2, 2022 · bfcc1fe · bfcc1fe
1 parent 5855b95
commit bfcc1fe
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diff --git a/example/Conv VAE MNIST example.ipynb b/example/Conv VAE MNIST example.ipynb
diff --git a/example/VAE MNIST example.ipynb b/example/VAE MNIST example.ipynb
diff --git a/example/VAE histone.ipynb b/example/VAE histone.ipynb
diff --git a/example/VAE iris example.ipynb b/example/VAE iris example.ipynb
diff --git a/scivae/vae.py b/scivae/vae.py
@@ -27,7 +27,6 @@
 import pickle
 from sklearn.preprocessing import MinMaxScaler
 from scivae.validate import Validate
-from tensorflow.keras.callbacks import TensorBoard
 import json
 from scivae import Loss
 from sciutil import SciException, SciUtil
@@ -559,8 +558,7 @@ def optimiser(self, optimiser_name: str, params: dict):
             return optimizers.Adamax(learning_rate=learning_rate, beta_1=beta_1, beta_2=beta_2)
 
         elif optimiser_name == 'adam':
-            return optimizers.Adam(learning_rate=learning_rate, beta_1=beta_1, decay=decay,
-                                   beta_2=beta_2, amsgrad=amsgrad)
+            return optimizers.Adam(learning_rate=learning_rate, beta_1=beta_1, beta_2=beta_2, amsgrad=amsgrad)
 
         elif optimiser_name == 'adadelta':
             return optimizers.Adadelta(learning_rate=learning_rate, rho=rho)

diff --git a/tests/data/sub_seqs_species.csv b/tests/data/sub_seqs_species.csv
diff --git a/tests/test_vae.py b/tests/test_vae.py
@@ -70,9 +70,9 @@ def test_histone_data(self):
         vis = Vis(vae, vae.u, None)
         vis.plot_node_hists(show_plt=True, save_fig=False)
         vis.plot_node_feature_correlation(vae_df, 'external_gene_name', columns=new_cols, show_plt=True, save_fig=False)
-
-        vis.plot_feature_scatters(vae_df, 'external_gene_name', columns=new_cols, show_plt=True, fig_type="png", save_fig=True,
-                                  title="latent space", output_dir='test_figures/')
+        #
+        # vis.plot_feature_scatters(vae_df, 'external_gene_name', columns=new_cols, show_plt=True, fig_type="png", save_fig=True,
+        #                           title="latent space", output_dir='test_figures/')
 
         cool_genes = [['Emx1', 'Eomes', 'Tbr1', 'Foxg1', 'Lhx6', 'Arx', 'Dlx1', 'Dlx2', 'Dlx5', 'Nr2e2', 'Otx2'],
                       ['Hoxd8', 'Hoxd9', 'Hoxd10', 'Hoxd11', 'Hoxd12', 'Hoxd13', 'Hoxa7', 'Hoxa9', 'Hoxa10', 'Hoxa11',