minor updates to interactive figures

dms-vep · Mar 19, 2024 · c199a4a · c199a4a
1 parent 8d8e72e
commit c199a4a
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Showing 84 changed files with 2,655 additions and 6,605 deletions.
diff --git a/custom_rules.smk b/custom_rules.smk
@@ -41,7 +41,6 @@ rule analyze_nipah_RBP_entry:
                 "combined_E2_E3_correlation_plots": output.combined_E2_E3_correlation_plots,
                 "nipah_config": input.nipah_config,
                 "altair_config": input.altair_config,
-                #"entropy_file": input.entropy_file,
                 "entry_region_boxplot_plot": output.entry_region_boxplot_plot,
                 "surface": input.surface,
                 "combined_region_barplot_output": output.combined_region_barplot_output,
@@ -57,19 +56,13 @@ rule analyze_nipah_RBP_entry:
 rule analyze_nipah_RBP_binding:
     """Analyze EFNB2 and EFNB3 binding"""
     input:
-        #func_scores_E2_file="results/func_effects/averages/CHO_EFNB2_low_func_effects.csv",
-        binding_E2_file="results/filtered_data/binding/E2_binding_filtered.csv",
-        #func_scores_E3_file="results/func_effects/averages/CHO_EFNB3_low_func_effects.csv",
-        binding_E3_file="results/filtered_data/binding/E3_binding_filtered.csv",
+        binding_E2_file="results/filtered_data/binding/e2_binding_filtered.csv",
+        binding_E3_file="results/filtered_data/binding/e3_binding_filtered.csv",
         nb="notebooks/ephrin_binding.ipynb",
         nipah_config="nipah_config.yaml",
         altair_config="data/custom_analyses_data/theme.py",
     output:
         nb="results/notebooks/ephrin_binding.ipynb",
-        #filtered_E2_binding_data="results/filtered_data/E2_binding_filtered.csv",
-        #filtered_E3_binding_data="results/filtered_data/E3_binding_filtered.csv",
-        #filtered_E2_binding_low_effect="results/filtered_data/E2_binding_low_effect_filter.csv",
-        #filtered_E3_binding_low_effect="results/filtered_data/E3_binding_low_effect_filter.csv",
         entry_binding_combined_corr_plot="results/images/entry_binding_combined_corr_plot.html",
         entry_binding_combined_corr_plot_agg="results/images/entry_binding_combined_corr_plot_agg.html",
         E2_E3_correlation="results/images/E2_E3_correlation.html",
@@ -82,21 +75,14 @@ rule analyze_nipah_RBP_binding:
         binding_region_bubble_plot="results/images/binding_region_bubble_plot.html",
         max_binding_in_contact="results/images/max_binding_in_contact.html",
         max_binding_in_stalk="results/images/max_binding_in_stalk.html",
+        combined_contact_ranked_bar_output='results/images/combined_contact_ranked_bar_output.html',
     params:
         yaml=lambda _, input, output: yaml.round_trip_dump(
             {
                 "nipah_config": input.nipah_config,
                 "altair_config": input.altair_config,
-                "entropy_file": input.entropy_file,
-                #"func_scores_E2_file": input.func_scores_E2_file,
                 "binding_E2_file": input.binding_E2_file,
-                #"func_scores_E3_file": input.func_scores_E3_file,
                 "binding_E3_file": input.binding_E3_file,
-
-                #"filtered_E2_binding_data": output.filtered_E2_binding_data,
-                #"filtered_E3_binding_data": output.filtered_E3_binding_data,
-                #"filtered_E2_binding_low_effect": output.filtered_E2_binding_low_effect,
-                #"filtered_E3_binding_low_effect": output.filtered_E3_binding_low_effect,
                 "entry_binding_combined_corr_plot": output.entry_binding_combined_corr_plot,
                 "entry_binding_combined_corr_plot_agg": output.entry_binding_combined_corr_plot_agg,
                 "E2_E3_correlation": output.E2_E3_correlation,
@@ -109,6 +95,7 @@ rule analyze_nipah_RBP_binding:
                 "binding_region_bubble_plot": output.binding_region_bubble_plot,
                 "max_binding_in_contact": output.max_binding_in_contact,
                 "max_binding_in_stalk": output.max_binding_in_stalk,
+                "combined_contact_ranked_bar_output": output.combined_contact_ranked_bar_output,
             }
         ),
     log:
@@ -521,7 +508,7 @@ rule filter_data:
         m102_filtered_path="results/filtered_data/escape/m102_escape_filtered.csv",
         HENV32_filtered_path="results/filtered_data/escape/HENV32_escape_filtered.csv",
         nAH1_filtered_path="results/filtered_data/escape/nAH1_escape_filtered.csv",
-        #e2_low_mab_effect_filter = 'results/filtered_data/escape/e2_low_mab_effect_filter.csv',
+        mab_filter_concat_file = 'results/filtered_data/escape/mab_filter_concat.csv',
         e3_low_mab_effect_filter = 'results/filtered_data/escape/e3_low_mab_effect_filter.csv'
 
     params:
@@ -552,8 +539,8 @@ rule filter_data:
                 "HENV32_filtered_path": output.HENV32_filtered_path,
                 "m102_filtered_path": output.m102_filtered_path,
                 "nAH1_filtered_path": output.nAH1_filtered_path,
-                #"e2_low_mab_effect_filter": output.e2_low_mab_effect_filter,
                 "e3_low_mab_effect_filter": output.e3_low_mab_effect_filter,
+                "mab_filter_concat_file": output.mab_filter_concat_file,
             }
         ),
     log:
@@ -629,7 +616,7 @@ rule make_heatmaps:
     input:
         nb="notebooks/plot_heatmaps.ipynb",
         nipah_config="nipah_config.yaml",
-        altair_config="data/custom_analyses_data/theme.py",
+        altair_config="data/custom_analyses_data/heatmap_theme.py",
         entropy_file="results/entropy/entropy.csv",
         func_scores_E2_file="results/filtered_data/entry/e2_entry_filtered.csv",
         func_scores_E3_file="results/filtered_data/entry/e3_entry_filtered.csv",
@@ -817,6 +804,7 @@ docs["Additional files and charts"] = {
         "Bubbleplot of binding scores by region": rules.analyze_nipah_RBP_binding.output.binding_region_bubble_plot,
         "Max Binding Scores in Contact Site": rules.analyze_nipah_RBP_binding.output.max_binding_in_contact,
         "Max Binding Scores in Stalk": rules.analyze_nipah_RBP_binding.output.max_binding_in_stalk,
+        "Contact ranked sites": rules.analyze_nipah_RBP_binding.output.combined_contact_ranked_bar_output,
         "Ephrin neutralization notebook": rules.ephrin_neuts.output.nb,
         "Ephrin neutralization curve plot": rules.ephrin_neuts.output.ephrin_curve_plot,
         "Ephrin Binding Validation Neut Curves Plots": {

diff --git a/data/custom_analyses_data/heatmap_theme.py b/data/custom_analyses_data/heatmap_theme.py
@@ -0,0 +1,94 @@
+import altair as alt
+
+def heatmap_theme():
+    # Typography
+    font = "Helvetica Light"
+    #labelFont = "Helvetica Light"
+
+    # Colors
+    main_palette = ["#1f4e79", "#ff7f0e", "#2ca02c", "#d62728", "#9467bd", "#8c564b", "#e377c2", "#7f7f7f", "#bcbd22", "#17becf"]
+    sequential_palette = ["#c7e9b4", "#7fcdbb", "#41b6c4", "#1d91c0", "#225ea8", "#253494"]
+
+    # Axes
+    axisColor = "#000000"
+    gridColor = "#DEDDDD"
+
+    return {
+        #"width": 400,
+        #"height": 400,
+        "config": {
+            "background": "transparent",
+            "title": {
+                "fontSize": 20,
+                "fontWeight": 'bold',
+                "font": font,
+                "anchor": "start",
+                "color": "#000000",
+                "orient": 'top',
+                "offset": 5,
+                "subtitleColor": 'gray',
+                "subtitleFont": font,
+                "subtitleFontWeight": 'normal',
+                "subtitleFontSize": 18,
+                "subtitlePadding": 2,
+            },
+            "axis": {
+                #domain
+                "domain": True,
+                "domainColor": axisColor,
+                "domainWidth": 1,
+                #grid
+                "grid": False,
+                "gridColor": gridColor,
+                "gridWidth": 0.5,
+                #label
+                "labelFont": font,
+                "labelFontSize": 12,
+                "labelFlush": False,
+                "labelFontWeight": 'normal',
+                "labelPadding": 2,
+                #"labelAngle": 0,
+
+                #ticks
+                "tickColor": axisColor,
+                "tickSize": 4,
+                #"tickCount": 3,
+                "tickWidth": 1,
+                #title
+                "titleFont": font,
+                "titleAlign": 'center',
+                "titleFontWeight": 'bold',
+                "titleFontSize": 14,
+                "titlePadding": 5,
+            },
+            "legend": {
+                "labelFont": font,
+                "labelFontSize": 14,
+                "symbolSize": 100,
+                "titleFont": font,
+                "titleFontSize": 14,
+                "titleFontWeight": 'bold',
+                "padding": 5,
+                "titleLimit": 200,
+                "gradientLength": 100,
+            },
+            "range": {
+                "category": main_palette,
+                "diverging": sequential_palette,
+            },
+            "view": {
+                "stroke": "transparent", # Remove the border around the visualization
+            	"strokeWidth": 0,
+            },
+        	"text": {
+            	"font": 'Helvetica Light',
+            	"fontSize": 14,
+        	}
+        }
+    }
+
+# Register the custom theme under a chosen name
+alt.themes.register('heatmap_theme', heatmap_theme)
+
+# Enable the newly registered theme
+alt.themes.enable('heatmap_theme')
diff --git a/data/custom_analyses_data/theme.py b/data/custom_analyses_data/theme.py
@@ -2,9 +2,8 @@
 
 def brendan_theme():
     # Typography
-    font = "Helvetica"
-    labelFont = "Helvetica Light"
-    sourceFont = "Helvetica"
+    font = "Helvetica Light"
+    #labelFont = "Helvetica Light"
 
     # Colors
     main_palette = ["#1f4e79", "#ff7f0e", "#2ca02c", "#d62728", "#9467bd", "#8c564b", "#e377c2", "#7f7f7f", "#bcbd22", "#17becf"]
@@ -21,55 +20,54 @@ def brendan_theme():
             "background": "transparent",
             "title": {
                 "fontSize": 20,
+                "fontWeight": 'bold',
                 "font": font,
                 "anchor": "start",
                 "color": "#000000",
                 "orient": 'top',
-                "offset": 10,
+                "offset": 5,
+                "subtitleColor": 'gray',
+                "subtitleFont": font,
+                "subtitleFontWeight": 'normal',
+                "subtitleFontSize": 18,
+                "subtitlePadding": 2,
             },
-            "axisX": {
+            "axis": {
+                #domain
                 "domain": True,
                 "domainColor": axisColor,
                 "domainWidth": 1,
+                #grid
                 "grid": False,
                 "gridColor": gridColor,
                 "gridWidth": 0.5,
-                "labelFont": labelFont,
-                "labelFontSize": 12,
-                "labelAngle": 0,
+                #label
+                "labelFont": font,
+                "labelFontSize": 14,
+                "labelFlush": False,
+                "labelFontWeight": 'normal',
+                "labelPadding": 2,
+                #"labelAngle": 0,
+
+                #ticks
                 "tickColor": axisColor,
                 "tickSize": 4,
-                "titleFont": font,
-                "tickCount": 3,
-                "tickWidth": 1,
-                "titleFontSize": 14,
-                "titlePadding": 5,
-            },
-            "axisY": {
-                "domain": True,
-                "domainColor": axisColor,
-                "domainWidth": 1,
-                "grid": False,
-                "gridColor": gridColor,
-                "gridWidth": 0.5,
-                "labelFont": labelFont,
-                "labelFontSize": 12,
-                "labelAngle": 0,
-                "tickColor": axisColor,
-                "tickSize": 4,
-                "tickCount": 3,
+                #"tickCount": 3,
                 "tickWidth": 1,
+                #title
                 "titleFont": font,
-                "titleFontSize":14,
+                "titleAlign": 'center',
+                "titleFontWeight": 'bold',
+                "titleFontSize": 14,
                 "titlePadding": 5,
-                "titleAngle": 270,
             },
             "legend": {
-                "labelFont": labelFont,
-                "labelFontSize": 12,
+                "labelFont": font,
+                "labelFontSize": 14,
                 "symbolSize": 100,
                 "titleFont": font,
                 "titleFontSize": 14,
+                "titleFontWeight": 'bold',
                 "padding": 5,
                 "titleLimit": 200,
                 "gradientLength": 100,
@@ -80,22 +78,17 @@ def brendan_theme():
             },
             "view": {
                 "stroke": "transparent", # Remove the border around the visualization
+            	"strokeWidth": 0,
             },
-            #"point": {
-            	#"filled": True,
-            	#"size": 25,
-            	#"opacity": 1,
-            	#"color": "black"
-            #},
-            #"boxplot": {
-            	#"extent": "min-max",
-            #	
-            #}
+        	"text": {
+            	"font": 'Helvetica Light',
+            	"fontSize": 14,
+        	}
         }
     }
 
 # Register the custom theme under a chosen name
-alt.themes.register('black_marks', brendan_theme)
+alt.themes.register('brendan_theme', brendan_theme)
 
 # Enable the newly registered theme
-alt.themes.enable('black_marks')
+alt.themes.enable('brendan_theme')
diff --git a/docs/htmls/CHO_EFNB2_all_corrs.html b/docs/htmls/CHO_EFNB2_all_corrs.html
diff --git a/docs/htmls/CHO_EFNB3_all_corrs.html b/docs/htmls/CHO_EFNB3_all_corrs.html
diff --git a/docs/htmls/CHO_corr_plot_save.html b/docs/htmls/CHO_corr_plot_save.html
diff --git a/docs/htmls/E2_E3_correlation.html b/docs/htmls/E2_E3_correlation.html
diff --git a/docs/htmls/E2_E3_correlation_site.html b/docs/htmls/E2_E3_correlation_site.html
diff --git a/docs/htmls/E2_E3_entry_all_muts_plot.html b/docs/htmls/E2_E3_entry_all_muts_plot.html
diff --git a/docs/htmls/E2_E3_entry_corr_plot.html b/docs/htmls/E2_E3_entry_corr_plot.html
diff --git a/docs/htmls/E2_binding_heatmap.html b/docs/htmls/E2_binding_heatmap.html
diff --git a/docs/htmls/E2_entry_heatmap.html b/docs/htmls/E2_entry_heatmap.html
diff --git a/docs/htmls/E3_binding_heatmap.html b/docs/htmls/E3_binding_heatmap.html
diff --git a/docs/htmls/E3_entry_heatmap.html b/docs/htmls/E3_entry_heatmap.html
diff --git a/docs/htmls/EFNB2_neut_corr.html b/docs/htmls/EFNB2_neut_corr.html
diff --git a/docs/htmls/EFNB3_neut_corr.html b/docs/htmls/EFNB3_neut_corr.html