change median to mean for calculating func scores and escape

dms-vep · Feb 29, 2024 · 1ea70be · 1ea70be
1 parent 9007f59
commit 1ea70be
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Showing 141 changed files with 135,096 additions and 135,106 deletions.
diff --git a/custom_rules.smk b/custom_rules.smk
@@ -384,16 +384,16 @@ rule make_files_for_mapping_structure:
         nAH13_infile='results/filtered_data/nAH1_escape_filtered.csv',
     output:
         nb="results/notebooks/mapping_site_level.ipynb",
-        E2_func_output="results/parsed_mapping_data/E2_entry_parsed.csv",
-        E2_binding_output="results/parsed_mapping_data/E2_binding_parsed.csv",
-        E3_func_output="results/parsed_mapping_data/E3_entry_parsed.csv",
-        E3_binding_output="results/parsed_mapping_data/E3_binding_parsed.csv",
-        HENV26_output='results/parsed_mapping_data/HENV26_escape_sum_parsed.csv',
-        HENV32_output='results/parsed_mapping_data/HENV32_escape_sum_parsed.csv',
-        HENV103_output='results/parsed_mapping_data/HENV103_escape_sum_parsed.csv',
-        HENV117_output='results/parsed_mapping_data/HENV117_escape_sum_parsed.csv',
-        m1024_output='results/parsed_mapping_data/m102_escape_sum_parsed.csv',
-        nAH13_output='results/parsed_mapping_data/nAH1_escape_sum_parsed.csv',
+        E2_func_output="results/parsed_mapping_data/E2_entry_mean.csv",
+        E2_binding_output="results/parsed_mapping_data/E2_binding_mean.csv",
+        E3_func_output="results/parsed_mapping_data/E3_entry_mean.csv",
+        E3_binding_output="results/parsed_mapping_data/E3_binding_mean.csv",
+        HENV26_output='results/parsed_mapping_data/HENV26_escape_mean.csv',
+        HENV32_output='results/parsed_mapping_data/HENV32_escape_mean.csv',
+        HENV103_output='results/parsed_mapping_data/HENV103_escape_mean.csv',
+        HENV117_output='results/parsed_mapping_data/HENV117_escape_mean.csv',
+        m1024_output='results/parsed_mapping_data/m102_escape_mean.csv',
+        nAH13_output='results/parsed_mapping_data/nAH1_escape_mean.csv',
 
     params:
         yaml=lambda _, input, output: yaml.round_trip_dump(

diff --git a/data/antibody_escape_config.yml b/data/antibody_escape_config.yml
@@ -959,7 +959,7 @@ avg_antibody_escape_default: &avg_antibody_escape_default
   icXX: 90
   escape_plot_kwargs:
     <<: *avg_escape_plot_kwargs_default
-    avg_type: median
+    avg_type: mean
     addtl_slider_stats:
       times_seen: 3
       escape_std: 2

diff --git a/data/func_effects_config.yml b/data/func_effects_config.yml
@@ -481,7 +481,7 @@ func_scores:
 
 # Define some defaults for each condition, used via the merge (<<) operator.
 avg_func_effects_default: &avg_func_effects_default
-  avg_method: median
+  avg_method: mean
   floor_for_effect_std: -2
   per_selection_tooltips: true
   plot_kwargs:

diff --git a/docs/htmls/293T_func_effects.html b/docs/htmls/293T_func_effects.html
diff --git a/docs/htmls/293T_latent_effects.html b/docs/htmls/293T_latent_effects.html
diff --git a/docs/htmls/CHO_EFNB2_high_func_effects.html b/docs/htmls/CHO_EFNB2_high_func_effects.html
diff --git a/docs/htmls/CHO_EFNB2_high_latent_effects.html b/docs/htmls/CHO_EFNB2_high_latent_effects.html
diff --git a/docs/htmls/CHO_EFNB2_low_func_effects.html b/docs/htmls/CHO_EFNB2_low_func_effects.html
diff --git a/docs/htmls/CHO_EFNB2_low_latent_effects.html b/docs/htmls/CHO_EFNB2_low_latent_effects.html
diff --git a/docs/htmls/CHO_EFNB2_medium_func_effects.html b/docs/htmls/CHO_EFNB2_medium_func_effects.html
diff --git a/docs/htmls/CHO_EFNB2_medium_latent_effects.html b/docs/htmls/CHO_EFNB2_medium_latent_effects.html
diff --git a/docs/htmls/CHO_EFNB3_high_func_effects.html b/docs/htmls/CHO_EFNB3_high_func_effects.html
diff --git a/docs/htmls/CHO_EFNB3_high_latent_effects.html b/docs/htmls/CHO_EFNB3_high_latent_effects.html
diff --git a/docs/htmls/CHO_EFNB3_low_func_effects.html b/docs/htmls/CHO_EFNB3_low_func_effects.html
diff --git a/docs/htmls/CHO_EFNB3_low_latent_effects.html b/docs/htmls/CHO_EFNB3_low_latent_effects.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_all_mut_effect.html b/docs/htmls/EFNB2_all_mut_effect.html
diff --git a/docs/htmls/EFNB2_dimeric_mut_effect.html b/docs/htmls/EFNB2_dimeric_mut_effect.html
diff --git a/docs/htmls/EFNB2_monomeric_mut_effect.html b/docs/htmls/EFNB2_monomeric_mut_effect.html
diff --git a/docs/htmls/EFNB3_dimeric_mut_effect.html b/docs/htmls/EFNB3_dimeric_mut_effect.html
diff --git a/docs/htmls/HENV103_mut_effect.html b/docs/htmls/HENV103_mut_effect.html
diff --git a/docs/htmls/HENV117_mut_effect.html b/docs/htmls/HENV117_mut_effect.html