Add font size sliders to plotting tabs

.gitignore

@@ -0,0 +1,2 @@
+__pycache__/
+*.pyc

server/anno_vs_anno_server.py

@@ -11,17 +11,26 @@ def anno_vs_anno_server(input, output, session, shared):
     @reactive.event(input.go_sk1, ignore_none=True)
     def spac_Sankey():
         adata = ad.AnnData(
-            X=shared['X_data'].get(), 
-            obs=pd.DataFrame(shared['obs_data'].get()), 
-            layers=shared['layers_data'].get(), 
+            X=shared['X_data'].get(),
+            obs=pd.DataFrame(shared['obs_data'].get()),
+            layers=shared['layers_data'].get(),
             dtype=shared['X_data'].get().dtype
         )
         if adata is not None:
             fig = spac.visualization.sankey_plot(
-                adata, 
-                source_annotation=input.sk1_anno1(), 
+                adata,
+                source_annotation=input.sk1_anno1(),
                 target_annotation=input.sk1_anno2()
             )
+
+            font_size = input.sankey_font_size()
+
+            # Modified... 
+            # Applying font size directly to the Sankey trace for node and 
+            # label text, as the global layout font can sometimes be ignored.
+            fig.update_layout(font=dict(size=font_size))
+            fig.update_traces(textfont=dict(size=font_size), selector=dict(type='sankey'))
+
             return fig
         return None
 
@@ -30,16 +39,29 @@ def spac_Sankey():
     @reactive.event(input.go_rhm1, ignore_none=True)
     def spac_Relational():
         adata = ad.AnnData(
-            X=shared['X_data'].get(), 
+            X=shared['X_data'].get(),
             obs=pd.DataFrame(shared['obs_data'].get())
         )
         if adata is not None:
             result = spac.visualization.relational_heatmap(
-                adata, 
-                source_annotation=input.rhm_anno1(), 
+                adata,
+                source_annotation=input.rhm_anno1(),
                 target_annotation=input.rhm_anno2()
             )
             shared['df_relational'].set(result['data'])
+
+            font_size = input.heatmap_font_size()
+
+            # Modified...
+            # Applying font size directly to the heatmap axes and color bar,
+            # as these elements often have their own font settings.
+            result['figure'].update_layout(
+                font=dict(size=font_size),
+                xaxis=dict(tickfont=dict(size=font_size)),
+                yaxis=dict(tickfont=dict(size=font_size))
+            )
+            result['figure'].update_coloraxes(colorbar_tickfont_size=font_size)
+
             return result['figure']
         return None
 
@@ -57,4 +79,4 @@ def download_df_1():
     def download_button_ui_1():
         if shared['df_relational'].get() is not None:
             return ui.download_button("download_df_1", "Download Data", class_="btn-warning")
-        return None
+        return None

server/annotations_server.py

@@ -1,6 +1,8 @@
 from shiny import ui, render, reactive
 import numpy as np
 import spac.visualization
+# Added...
+import matplotlib.pyplot as plt
 
 def annotations_server(input, output, session, shared):
     @output
@@ -11,30 +13,38 @@ def spac_Histogram_2():
         if adata is None:
             return None
 
+        # Added...
+        # Note: This assumes your UI file has a slider with the id 'annotations_font_size'.
+        # Please ensure this ID matches the one in your annotations_ui.py file.
+        font_size = input.annotations_font_size()
+        plt.rcParams.update({'font.size': font_size})
+        rotation = input.anno_slider()
+
         # 1) If "Group By" is UNCHECKED, show a simple annotation histogram
         if not input.h2_group_by_check():
             fig, ax, df = spac.visualization.histogram(
                 adata,
                 annotation=input.h2_anno()
             ).values()
-            shared['df_histogram2'].set(df) 
-            ax.tick_params(axis='x', rotation=input.anno_slider(), labelsize=10)
+            shared['df_histogram2'].set(df)
+            # Modified...
+            ax.tick_params(axis='x', rotation=rotation, labelsize=font_size)
             return fig
 
-        # 2) If "Group By" is CHECKED, we must always supply a 
+        # 2) If "Group By" is CHECKED, we must always supply a
         #    valid multiple parameter
         else:
-            # If user also checked "Plot Together", use their selected 
+            # If user also checked "Plot Together", use their selected
             # stack type
             if input.h2_together_check():
                 # e.g. 'stack', 'dodge', etc.
-                multiple_param = input.h2_together_drop()  
+                multiple_param = input.h2_together_drop()
 
                 together_flag = True
             else:
                 # If grouping by but not "plot together", pick a default layout
                 # or 'dodge' or any valid string
-                multiple_param = "layer"  
+                multiple_param = "layer"
                 together_flag = False
 
             fig, ax, df = spac.visualization.histogram(
@@ -44,13 +54,15 @@ def spac_Histogram_2():
                 together=together_flag,
                 multiple=multiple_param
             ).values()
-            shared['df_histogram2'].set(df) 
+            shared['df_histogram2'].set(df)
             axes = ax if isinstance(ax, (list, np.ndarray)) else [ax]
-            for ax in axes:
-                ax.tick_params(
-                    axis='x', 
-                    rotation=input.anno_slider(), 
-                    labelsize=10
+            # Modified... (renamed loop variable to avoid shadowing)
+            for current_ax in axes:
+                # Modified...
+                current_ax.tick_params(
+                    axis='x',
+                    rotation=rotation,
+                    labelsize=font_size
                 )
             return fig
         return None
@@ -61,16 +73,16 @@ def spac_Histogram_2():
     def download_histogram_button_ui():
         if shared['df_histogram2'].get() is not None:
             return ui.download_button(
-                "download_histogram2_df", 
-                "Download Data", 
+                "download_histogram2_df",
+                "Download Data",
                 class_="btn-warning"
             )
         return None
 
 
     @render.download(filename="annotation_histogram_data.csv")
     def download_histogram2_df():
-        df = shared['df_histogram2'].get()
+        df = shared['df_human_histogram2'].get()
         if df is not None:
             csv_string = df.to_csv(index=False)
             csv_bytes = csv_string.encode("utf-8")
@@ -86,8 +98,8 @@ def histogram_reactivity_2():
 
         if btn and not ui_initialized:
             dropdown = ui.input_select(
-                "h2_anno_1", 
-                "Select an Annotation", 
+                "h2_anno_1",
+                "Select an Annotation",
                 choices=shared['obs_names'].get()
             )
             ui.insert_ui(
@@ -97,8 +109,8 @@ def histogram_reactivity_2():
             )
 
             together_check = ui.input_checkbox(
-                "h2_together_check", 
-                "Plot Together", 
+                "h2_together_check",
+                "Plot Together",
                 value=True
             )
             ui.insert_ui(
@@ -120,18 +132,18 @@ def histogram_reactivity_2():
     def update_stack_type_dropdown():
         if input.h2_together_check():
             dropdown_together = ui.input_select(
-                "h2_together_drop", 
-                "Select Stack Type", 
-                choices=['stack', 'layer', 'dodge', 'fill'], 
+                "h2_together_drop",
+                "Select Stack Type",
+                choices=['stack', 'layer', 'dodge', 'fill'],
                 selected='stack'
             )
             ui.insert_ui(
                 ui.div({
-                    "id": "inserted-dropdown_together-1"}, 
+                    "id": "inserted-dropdown_together-1"},
                     dropdown_together
                 ),
                 selector="#main-h2_together_drop",
                 where="beforeEnd"
-            )      
+            )
         else:
-            ui.remove_ui("#inserted-dropdown_together-1")
+            ui.remove_ui("#inserted-dropdown_together-1")

server/boxplot_server.py

@@ -3,6 +3,8 @@
 import anndata as ad
 import pandas as pd
 import spac.visualization
+# Added...
+import matplotlib.pyplot as plt
 
 
 def boxplot_server(input, output, session, shared):
@@ -32,34 +34,38 @@ def spac_Boxplot():
 
         if not input.bp_output_type():
             return None
-        else: 
+        else:
 
             adata = ad.AnnData(
-                X=shared['X_data'].get(), 
-                obs=pd.DataFrame(shared['obs_data'].get()), 
-                var=pd.DataFrame(shared['var_data'].get()), 
-                layers=shared['layers_data'].get(), 
+                X=shared['X_data'].get(),
+                obs=pd.DataFrame(shared['obs_data'].get()),
+                var=pd.DataFrame(shared['var_data'].get()),
+                layers=shared['layers_data'].get(),
                 dtype=shared['X_data'].get().dtype
             )
+            # Added...
+            font_size = input.bp_font_size()
 
             # Proceed only if adata is valid
             if adata is not None and adata.var is not None:
 
                 fig, df = spac.visualization.boxplot_interactive(
-                    adata, 
-                    annotation=on_anno_check(), 
-                    layer=on_layer_check(), 
+                    adata,
+                    annotation=on_anno_check(),
+                    layer=on_layer_check(),
                     features=list(input.bp_features()),
                     showfliers=on_outlier_check(),
                     log_scale=input.bp_log_scale(),
                     orient=on_orient_check(),
-                    figure_height=3, 
-                    figure_width=4.8, 
+                    figure_height=3,
+                    figure_width=4.8,
                     figure_type="interactive"
                 ).values()
 
                 # Return the interactive Plotly figure object
                 shared['df_boxplot'].set(df)
+                # Added...
+                fig.update_layout(font=dict(size=font_size))
                 print(type(fig))
                 return fig
 
@@ -81,8 +87,8 @@ def download_boxplot():
     def download_button_ui1():
         if shared['df_boxplot'].get() is not None:
             return ui.download_button(
-                "download_boxplot", 
-                "Download Data", 
+                "download_boxplot",
+                "Download Data",
                 class_="btn-warning"
             )
         return None
@@ -101,33 +107,35 @@ def boxplot_static():
         if input.bp_output_type():
             return None
 
-        else: 
+        else:
 
             adata = ad.AnnData(
-                X=shared['X_data'].get(), 
-                obs=pd.DataFrame(shared['obs_data'].get()), 
-                var=pd.DataFrame(shared['var_data'].get()), 
-                layers=shared['layers_data'].get(), 
+                X=shared['X_data'].get(),
+                obs=pd.DataFrame(shared['obs_data'].get()),
+                var=pd.DataFrame(shared['var_data'].get()),
+                layers=shared['layers_data'].get(),
                 dtype=shared['X_data'].get().dtype
             )
+            # Added...
+            font_size = input.bp_font_size()
 
             # Proceed only if adata is valid
             if adata is not None and adata.var is not None:
-                
+
                 fig, df = spac.visualization.boxplot_interactive(
-                    adata, 
-                    annotation=on_anno_check(), 
-                    layer=on_layer_check(), 
+                    adata,
+                    annotation=on_anno_check(),
+                    layer=on_layer_check(),
                     features=list(input.bp_features()),
                     showfliers=on_outlier_check(),
                     log_scale=input.bp_log_scale(),
                     orient=on_orient_check(),
-                    figure_height=3, 
-                    figure_width=4.8, 
+                    figure_height=3,
+                    figure_width=4.8,
                     figure_type="static"
                 ).values()
-
+                # Added...
+                fig.update_layout(font=dict(size=font_size))
                 return fig
 
-        return None
-
+        return None