Rename pages/4mwt_aniridia.py to pages/aniridia_integrated.py

pages/{4mwt_aniridia.py → aniridia_integrated.py}

@@ -13,7 +13,7 @@ pl.enable_string_cache(False)
 
 dash.register_page(__name__, location="sidebar")
 
-dataset = "dataaniridia/4mwt/sc_liu_aniridia_4mwt_processed"
+dataset = "dataaniridia/integrated/sc_liu_aniridia_integrated_processed"
 
 # Set custom resolution for plots:
 config_fig = {
@@ -113,51 +113,51 @@ tab1_content = html.Div([
                  options=df.columns),
     html.Label("N Genes by Counts"),
     dcc.RangeSlider(
-        id='range-slider_db3-1',
+        id='range-slider-1',
         step=250,
         value=[min_value, max_value],
         marks={i: str(i) for i in range(min_value, max_value + 1, 250)},
     ),
-    dcc.Input(id='min-slider_db3-1', type='number', value=min_value, debounce=True),
-    dcc.Input(id='max-slider_db3-1', type='number', value=max_value, debounce=True),
+    dcc.Input(id='min-slider-1', type='number', value=min_value, debounce=True),
+    dcc.Input(id='max-slider-1', type='number', value=max_value, debounce=True),
     html.Label("Total Counts"),
     dcc.RangeSlider(
-        id='range-slider_db3-2',
+        id='range-slider-2',
         step=7500,
         value=[min_value_2, max_value_2],
         marks={i: str(i) for i in range(min_value_2, max_value_2 + 1, 7500)},
     ),
-    dcc.Input(id='min-slider_db3-2', type='number', value=min_value_2, debounce=True),
-    dcc.Input(id='max-slider_db3-2', type='number', value=max_value_2, debounce=True),
+    dcc.Input(id='min-slider-2', type='number', value=min_value_2, debounce=True),
+    dcc.Input(id='max-slider-2', type='number', value=max_value_2, debounce=True),
     html.Label("Percent Mitochondrial Genes"),
     dcc.RangeSlider(
-        id='range-slider_db3-3',
+        id='range-slider-3',
         step=5,
         min=0,
         max=100,
         value=[min_value_3, max_value_3],
     ),
-    dcc.Input(id='min-slider_db3-3', type='number', value=min_value_3, debounce=True),
-    dcc.Input(id='max-slider_db3-3', type='number', value=max_value_3, debounce=True),
+    dcc.Input(id='min-slider-3', type='number', value=min_value_3, debounce=True),
+    dcc.Input(id='max-slider-3', type='number', value=max_value_3, debounce=True),
     html.Div([
-        dcc.Graph(id='pie-graph_db3', figure={}, className='four columns',config=config_fig),
-        dcc.Graph(id='my-graph_db3', figure={}, clickData=None, hoverData=None,
+        dcc.Graph(id='pie-graph', figure={}, className='four columns',config=config_fig),
+        dcc.Graph(id='my-graph', figure={}, clickData=None, hoverData=None,
                   className='four columns',config=config_fig
                   ),
-        dcc.Graph(id='scatter-plot_db3', figure={}, className='four columns',config=config_fig)
+        dcc.Graph(id='scatter-plot', figure={}, className='four columns',config=config_fig)
     ]),
     html.Div([
-        dcc.Graph(id='scatter-plot_db3-2', figure={}, className='four columns',config=config_fig)
+        dcc.Graph(id='scatter-plot-2', figure={}, className='four columns',config=config_fig)
     ]),
     html.Div([
-        dcc.Graph(id='scatter-plot_db3-3', figure={}, className='four columns',config=config_fig)
+        dcc.Graph(id='scatter-plot-3', figure={}, className='four columns',config=config_fig)
     ]),
     html.Div([
-        dcc.Graph(id='scatter-plot_db3-4', figure={}, className='four columns',config=config_fig)
+        dcc.Graph(id='scatter-plot-4', figure={}, className='four columns',config=config_fig)
     ]),
 ])
 
-# Create the second tab content with scatter-plot_db3-5 and scatter-plot_db3-6
+# Create the second tab content with scatter-plot-5 and scatter-plot-6
 tab2_content = html.Div([
     html.Div([
             html.Label("S-cycle genes"),
@@ -264,23 +264,22 @@ tab2_content = html.Div([
     "Psrc1",
     "Gas2l3"
 ]),
-
     ]),
     html.Div([
-        dcc.Graph(id='scatter-plot_db3-5', figure={}, className='three columns',config=config_fig)
+        dcc.Graph(id='scatter-plot-5', figure={}, className='three columns',config=config_fig)
     ]),
     html.Div([
-        dcc.Graph(id='scatter-plot_db3-6', figure={}, className='three columns',config=config_fig)
+        dcc.Graph(id='scatter-plot-6', figure={}, className='three columns',config=config_fig)
     ]),
     html.Div([
-        dcc.Graph(id='scatter-plot_db3-7', figure={}, className='three columns',config=config_fig)
+        dcc.Graph(id='scatter-plot-7', figure={}, className='three columns',config=config_fig)
     ]),
     html.Div([
-        dcc.Graph(id='scatter-plot_db3-8', figure={}, className='three columns',config=config_fig)
+        dcc.Graph(id='scatter-plot-8', figure={}, className='three columns',config=config_fig)
     ]),
 ])
 
-# Create the second tab content with scatter-plot_db3-5 and scatter-plot_db3-6
+# Create the second tab content with scatter-plot-5 and scatter-plot-6
 tab3_content = html.Div([
     html.Div([
             html.Label("UMAP condition 1"),
@@ -290,23 +289,23 @@ tab3_content = html.Div([
             dcc.Dropdown(id='dpdn6', value="n_genes_by_counts", multi=False,
                  options=df.columns),
     html.Div([
-        dcc.Graph(id='scatter-plot_db3-9', figure={}, className='four columns',config=config_fig)
+        dcc.Graph(id='scatter-plot-9', figure={}, className='four columns',config=config_fig)
     ]),
     html.Div([
-        dcc.Graph(id='scatter-plot_db3-10', figure={}, className='four columns',config=config_fig)
+        dcc.Graph(id='scatter-plot-10', figure={}, className='four columns',config=config_fig)
     ]),
     html.Div([
-        dcc.Graph(id='scatter-plot_db3-11', figure={}, className='four columns',config=config_fig)
+        dcc.Graph(id='scatter-plot-11', figure={}, className='four columns',config=config_fig)
     ]),
     html.Div([
-            dcc.Graph(id='my-graph_db32', figure={}, clickData=None, hoverData=None,
+            dcc.Graph(id='my-graph2', figure={}, clickData=None, hoverData=None,
                   className='four columns',config=config_fig
                   )
     ]),
     ]),
 ])
 #    html.Div([
-#        dcc.Graph(id='scatter-plot_db3-12', figure={}, className='four columns',config=config_fig)
+#        dcc.Graph(id='scatter-plot-12', figure={}, className='four columns',config=config_fig)
 #    ]),
 
 
@@ -317,7 +316,7 @@ tab4_content = html.Div([
                  options=df.columns),
 ]),
     html.Div([
-        dcc.Graph(id='scatter-plot_db3-12', figure={}, className='row',style={'width': '100vh', 'height': '90vh'}),  # px)
+        dcc.Graph(id='scatter-plot-12', figure={}, className='row',style={'width': '100vh', 'height': '90vh'}),  # px)
     ]),
 ])
 
@@ -337,63 +336,61 @@ layout = html.Div([
 
 # Define the circular callback
 @callback(
-    Output("min-slider_db3-1", "value"),
-    Output("max-slider_db3-1", "value"),
-    Output("min-slider_db3-2", "value"),
-    Output("max-slider_db3-2", "value"),
-    Output("min-slider_db3-3", "value"),
-    Output("max-slider_db3-3", "value"),
-    Input("min-slider_db3-1", "value"),
-    Input("max-slider_db3-1", "value"),
-    Input("min-slider_db3-2", "value"),
-    Input("max-slider_db3-2", "value"),
-    Input("min-slider_db3-3", "value"),
-    Input("max-slider_db3-3", "value"),
-     
+    Output("min-slider-1", "value"),
+    Output("max-slider-1", "value"),
+    Output("min-slider-2", "value"),
+    Output("max-slider-2", "value"),
+    Output("min-slider-3", "value"),
+    Output("max-slider-3", "value"),
+    Input("min-slider-1", "value"),
+    Input("max-slider-1", "value"),
+    Input("min-slider-2", "value"),
+    Input("max-slider-2", "value"),
+    Input("min-slider-3", "value"),
+    Input("max-slider-3", "value"),
 )
 def circular_callback(min_1, max_1, min_2, max_2, min_3, max_3):
     return min_1, max_1, min_2, max_2, min_3, max_3
 
 @callback(
-    Output('range-slider_db3-1', 'value'),
-    Output('range-slider_db3-2', 'value'),
-    Output('range-slider_db3-3', 'value'),
-    Input('min-slider_db3-1', 'value'),
-    Input('max-slider_db3-1', 'value'),
-    Input('min-slider_db3-2', 'value'),
-    Input('max-slider_db3-2', 'value'),
-    Input('min-slider_db3-3', 'value'),
-    Input('max-slider_db3-3', 'value'),
-     
+    Output('range-slider-1', 'value'),
+    Output('range-slider-2', 'value'),
+    Output('range-slider-3', 'value'),
+    Input('min-slider-1', 'value'),
+    Input('max-slider-1', 'value'),
+    Input('min-slider-2', 'value'),
+    Input('max-slider-2', 'value'),
+    Input('min-slider-3', 'value'),
+    Input('max-slider-3', 'value'),    
 )
 def update_slider_values(min_1, max_1, min_2, max_2, min_3, max_3):
     return [min_1, max_1], [min_2, max_2], [min_3, max_3]
 
 @callback(
-    Output(component_id='my-graph_db3', component_property='figure'),
-    Output(component_id='pie-graph_db3', component_property='figure'),
-    Output(component_id='scatter-plot_db3', component_property='figure'),
-    Output(component_id='scatter-plot_db3-2', component_property='figure'),
-    Output(component_id='scatter-plot_db3-3', component_property='figure'),
-    Output(component_id='scatter-plot_db3-4', component_property='figure'),  # Add this new scatter plot
-    Output(component_id='scatter-plot_db3-5', component_property='figure'),
-    Output(component_id='scatter-plot_db3-6', component_property='figure'),
-    Output(component_id='scatter-plot_db3-7', component_property='figure'),
-    Output(component_id='scatter-plot_db3-8', component_property='figure'),
-    Output(component_id='scatter-plot_db3-9', component_property='figure'),
-    Output(component_id='scatter-plot_db3-10', component_property='figure'),
-    Output(component_id='scatter-plot_db3-11', component_property='figure'),
-    Output(component_id='scatter-plot_db3-12', component_property='figure'),
-    Output(component_id='my-graph_db32', component_property='figure'),
+    Output(component_id='my-graph', component_property='figure'),
+    Output(component_id='pie-graph', component_property='figure'),
+    Output(component_id='scatter-plot', component_property='figure'),
+    Output(component_id='scatter-plot-2', component_property='figure'),
+    Output(component_id='scatter-plot-3', component_property='figure'),
+    Output(component_id='scatter-plot-4', component_property='figure'),  # Add this new scatter plot
+    Output(component_id='scatter-plot-5', component_property='figure'),
+    Output(component_id='scatter-plot-6', component_property='figure'),
+    Output(component_id='scatter-plot-7', component_property='figure'),
+    Output(component_id='scatter-plot-8', component_property='figure'),
+    Output(component_id='scatter-plot-9', component_property='figure'),
+    Output(component_id='scatter-plot-10', component_property='figure'),
+    Output(component_id='scatter-plot-11', component_property='figure'),
+    Output(component_id='scatter-plot-12', component_property='figure'),
+    Output(component_id='my-graph2', component_property='figure'),
     Input(component_id='dpdn2', component_property='value'),
     Input(component_id='dpdn3', component_property='value'),
     Input(component_id='dpdn4', component_property='value'),
     Input(component_id='dpdn5', component_property='value'),
     Input(component_id='dpdn6', component_property='value'),
     Input(component_id='dpdn7', component_property='value'),
-    Input(component_id='range-slider_db3-1', component_property='value'),
-    Input(component_id='range-slider_db3-2', component_property='value'),
-    Input(component_id='range-slider_db3-3', component_property='value'),
+    Input(component_id='range-slider-1', component_property='value'),
+    Input(component_id='range-slider-2', component_property='value'),
+    Input(component_id='range-slider-3', component_property='value'),
      
 )
 
@@ -415,7 +412,7 @@ def update_graph_and_pie_chart(col_chosen, s_chosen, g2m_chosen, condition1_chos
     dff = dff.sort(col_chosen)
     
     # Plot figures
-    fig_violin_db3 = px.violin(data_frame=dff, x=col_chosen, y=col_features, box=True, points="all",
+    fig_violin = px.violin(data_frame=dff, x=col_chosen, y=col_features, box=True, points="all",
                             color=col_chosen, hover_name=col_chosen,template="seaborn")
 
     # Cache commonly used subexpressions
@@ -470,70 +467,70 @@ def update_graph_and_pie_chart(col_chosen, s_chosen, g2m_chosen, condition1_chos
     #expression_means = expression_means.select(["batch", "Gene", "Expression"] + condition3_chosen)
     category_counts = category_counts.sort(col_chosen)
     
-    fig_pie_db3 = px.pie(category_counts, values="normalized_count", names=col_chosen, labels=col_chosen, hole=.3, title=pie_title, template="seaborn")
+    fig_pie = px.pie(category_counts, values="normalized_count", names=col_chosen, labels=col_chosen, hole=.3, title=pie_title, template="seaborn")
 
     #labels = category_counts[col_chosen].to_list()
     #values = category_counts["normalized_count"].to_list()
 
     # Create the scatter plots
-    fig_scatter_db3 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=col_chosen,
+    fig_scatter = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=col_chosen,
                              labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                              hover_name='batch',template="seaborn")
 
-    fig_scatter_db3_2 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=col_mt,
+    fig_scatter_2 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=col_mt,
                              labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                              hover_name='batch',template="seaborn")
 
-    fig_scatter_db3_3 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=col_features,
+    fig_scatter_3 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=col_features,
                              labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                              hover_name='batch',template="seaborn")
 
 
-    fig_scatter_db3_4 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=col_counts,
+    fig_scatter_4 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=col_counts,
                              labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                              hover_name='batch',template="seaborn")
     
-    fig_scatter_db3_5 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=s_chosen,
+    fig_scatter_5 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=s_chosen,
                             labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                             hover_name='batch', title="S-cycle gene:",template="seaborn")
 
-    fig_scatter_db3_6 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=g2m_chosen,
+    fig_scatter_6 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=g2m_chosen,
                             labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                             hover_name='batch', title="G2M-cycle gene:",template="seaborn")
     
-    fig_scatter_db3_7 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color="S_score",
+    fig_scatter_7 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color="S_score",
                             labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                             hover_name='batch', title="S score:",template="seaborn")
     
-    fig_scatter_db3_8 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color="G2M_score",
+    fig_scatter_8 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color="G2M_score",
                             labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                             hover_name='batch', title="G2M score:",template="seaborn")
 
     # Sort values of custom in-between
     dff = dff.sort(condition1_chosen)
     
-    fig_scatter_db3_9 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=condition1_chosen,
+    fig_scatter_9 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=condition1_chosen,
                             labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                             hover_name='batch',template="seaborn")
     
-    fig_scatter_db3_10 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=condition2_chosen,
+    fig_scatter_10 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=condition2_chosen,
                             labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                             hover_name='batch',template="seaborn")
     
-    fig_scatter_db3_11 = px.scatter(data_frame=dff, x=condition1_chosen, y=condition2_chosen, color=condition1_chosen,
+    fig_scatter_11 = px.scatter(data_frame=dff, x=condition1_chosen, y=condition2_chosen, color=condition1_chosen,
                             #labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                             hover_name='batch',template="seaborn")
     
-    fig_scatter_db3_12 = px.scatter(data_frame=expression_means, x="Gene", y=col_chosen, color="Mean expression",
+    fig_scatter_12 = px.scatter(data_frame=expression_means, x="Gene", y=col_chosen, color="Mean expression",
                                 size="percentage", size_max = 20,
                             #labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                             hover_name=col_chosen,template="seaborn")
     
-    fig_violin_db32 = px.violin(data_frame=dff, x=condition1_chosen, y=condition2_chosen, box=True, points="all",
+    fig_violin2 = px.violin(data_frame=dff, x=condition1_chosen, y=condition2_chosen, box=True, points="all",
                             color=condition1_chosen, hover_name=condition1_chosen,template="seaborn")
 
 
-    return fig_violin_db3, fig_pie_db3, fig_scatter_db3, fig_scatter_db3_2, fig_scatter_db3_3, fig_scatter_db3_4, fig_scatter_db3_5, fig_scatter_db3_6, fig_scatter_db3_7, fig_scatter_db3_8, fig_scatter_db3_9, fig_scatter_db3_10, fig_scatter_db3_11, fig_scatter_db3_12, fig_violin_db32
+    return fig_violin, fig_pie, fig_scatter, fig_scatter_2, fig_scatter_3, fig_scatter_4, fig_scatter_5, fig_scatter_6, fig_scatter_7, fig_scatter_8, fig_scatter_9, fig_scatter_10, fig_scatter_11, fig_scatter_12, fig_violin2
 
 # Set http://localhost:5000/ in web browser
 # Now create your regular FASTAPI application