add missing packages to environment.yml

fix extracted path in figure files

analysis/extended_figures/figure_ed5_importance.py

@@ -247,12 +247,12 @@ def plot_high_genes2(ax, layer=1, graph ='hist', direction='h'):
     else:
         column = 'coef'
 
-    node_importance = pd.read_csv(join(module_path,'./extracted/node_importance_graph_adjusted.csv'), index_col=0)
+    node_importance = pd.read_csv(join(module_path,'./figure_3/extracted/node_importance_graph_adjusted.csv'), index_col=0)
     high_nodes = node_importance[node_importance.layer == layer].abs().nlargest(10, columns=[column])
     # high_nodes = node_importance[node_importance.layer == layer].abs().nlargest(10, columns=['coef'])
     features = list(high_nodes.index)
-    response = pd.read_csv(join(module_path,'./extracted/response.csv'), index_col=0)
-    df_in = pd.read_csv(join(module_path, './extracted/gradient_importance_detailed_{}.csv').format(layer), index_col=0)
+    response = pd.read_csv(join(module_path,'./figure_3/extracted/response.csv'), index_col=0)
+    df_in = pd.read_csv(join(module_path, './figure_3/extracted/gradient_importance_detailed_{}.csv').format(layer), index_col=0)
     df_in = df_in.copy()
     df_in = df_in.join(response)
     df_in['group'] = df_in.response
@@ -395,8 +395,8 @@ def shorten_names(name):
 fontproperties = {'family': 'Arial', 'weight': 'normal', 'size': 6}
 
 def plot_axis(axis):
-    node_importance = pd.read_csv(join(module_path,'extracted/node_importance_graph_adjusted.csv'), index_col=0)
-    response = pd.read_csv(join(module_path, 'extracted/response.csv'), index_col=0)
+    node_importance = pd.read_csv(join(module_path,'figure_3/extracted/node_importance_graph_adjusted.csv'), index_col=0)
+    response = pd.read_csv(join(module_path, 'figure_3/extracted/response.csv'), index_col=0)
     print response.head()
     layers = sorted(list(node_importance.layer.unique()))
     print layers

analysis/extended_figures/figure_ed7_activation.py

@@ -70,9 +70,9 @@ def corrfunc(x, y, **kws):
 
 def plot_activation(ax, column='coef_combined', layer=3, pad=200):
 
-    node_activation = pd.read_csv(join(module_path,'extracted/node_importance_graph_adjusted.csv'), index_col=0)
-    response = pd.read_csv(join(module_path,'extracted/response.csv'), index_col=0)
-    df = pd.read_csv(join(module_path,'extracted/activation_{}.csv'.format(layer)), index_col=0)
+    node_activation = pd.read_csv(join(module_path,'figure_3/extracted/node_importance_graph_adjusted.csv'), index_col=0)
+    response = pd.read_csv(join(module_path,'figure_3/extracted/response.csv'), index_col=0)
+    df = pd.read_csv(join(module_path,'figure_3/extracted/activation_{}.csv'.format(layer)), index_col=0)
     df.columns = get_pathway_names(df.columns)
     if layer==1:
         column='coef_combined'

analysis/figure_3/figure_3_sankey.py

@@ -1,4 +1,6 @@
 from os.path import dirname, realpath
+
+from config_path import PATHWAY_PATH
 from setup import saving_dir
 from analysis.vis_utils import get_reactome_pathway_names
 
@@ -543,8 +545,8 @@ def get_fromated_network(links, high_nodes_df, col_name, remove_others):
     # shorten names
 
     def get_short_names(all_node_labels):
-        '/Users/haithamelmarakeby/PycharmProjects/pnet2/analysis/figure_3/extracted/pathways_short_names.xlsx'
-        df = pd.read_excel(join(module_path, './extracted/pathways_short_names.xlsx'), index_col=0)
+
+        df = pd.read_excel(join(PATHWAY_PATH, 'pathways_short_names.xlsx'), index_col=0)
         mapping_dict = {}
         for k, v in zip(df['Full name'].values, df['Short name (Eli)'].values):
             mapping_dict[k] = str(v)

environment.yml

@@ -6,7 +6,7 @@ dependencies:
   - pip=18.1
   - enum34=1.1.6
   - futures=3.3.0
-  - h5py=2.9.0
+  - h5py=2.9.0l.c
   - hdf5=1.10.4
   - imageio=2.6.1
   - keras=2.2.4
@@ -27,9 +27,12 @@ dependencies:
   - tensorboard=1.12.2
   - tensorflow=1.12.0
   - yaml=0.1.7
+  - plotly-orca=1.3.1
   - pip:
+    - adjusttext==0.7.3
     - lifelines==0.19.5
     - matplotlib==2.2.4
+    - psutil==5.8.0
     - networkx==2.2
     - pyvis==0.1.7.0
     - requests==2.23.0