rename argments

kojikoji · Nov 11, 2021 · a20dece · a20dece
1 parent 12e4807
commit a20dece
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Showing 3 changed files with 4 additions and 5 deletions.
diff --git a/setup.cfg b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = vicdyf
-version=0.0.6
+version=0.0.8
 author = Kojima Yasuhiro
 author_email = [email protected]
 description = Estimate cell state dynamics with fluctuation

diff --git a/src/vicdyf/modules.py b/src/vicdyf/modules.py
@@ -77,7 +77,7 @@ def __init__(
         super(VicDyf, self).__init__()
         self.enc_z = Encoder(num_enc_z_layers, x_dim, enc_z_h_dim, z_dim)
         self.enc_d = Encoder(num_enc_d_layers, z_dim, enc_d_h_dim, z_dim)
-        self.dec_z = Decoder(num_enc_z_layers, z_dim, dec_z_h_dim, x_dim)
+        self.dec_z = Decoder(num_dec_z_layers, z_dim, dec_z_h_dim, x_dim)
         self.dt = 1
         self.gamma_mean = 0.05
         self.d_coeff = 0.01

diff --git a/tutorial/application_on_pancreas.py b/tutorial/application_on_pancreas.py
@@ -7,8 +7,7 @@
 raw_adata = scv.datasets.pancreas()
 adata.layers['spliced'] = raw_adata[:, adata.var_names].layers['spliced']
 adata.layers['unspliced'] = raw_adata[:, adata.var_names].layers['unspliced']
-adata = vicdyf.workflow.estimate_dynamics(adata)#, first_epoch=10, second_epoch=10)
-adata = vicdyf.utils.change_visualization(adata, n_neighbors=100)
-adata = vicdyf.utils.change_visualization(adata, embeddings='X_vicdyf_umap')
+adata = vicdyf.workflow.estimate_dynamics(adata)
+adata = vicdyf.utils.change_visualization(adata, n_neighbors=30)
 scv.pl.velocity_embedding_grid(adata,X=adata.obsm['X_vicdyf_umap'], V=adata.obsm['X_vicdyf_mdumap'], color='vicdyf_fluctuation', show=False, basis='X_vicdyf_umap', density=0.3)
 plt.savefig('tutorial/pancreas_flow.png')