renamed count_vars_ML previous version as such

scripts/plotting/plotting_thesis/katg/gg_pairs_all_katg.R

@@ -1,6 +1,13 @@
-#source("~/git/LSHTM_analysis/config/katg.R")
-#source("~/git/LSHTM_analysis/scripts/plotting/plotting_colnames.R")
-#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
+source("~/git/LSHTM_analysis/config/katg.R")
+source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
+
+#=======
+# output
+#=======
+outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
+cat("plots will output to:", outdir_images)
+
+
 
 my_gg_pairs=function(plot_df, plot_title
                      , tt_args_size = 2.5
@@ -85,7 +92,7 @@ unmasked_vals
 # Stability
 #================
 corr_ps_colnames = c(static_cols
-                     , "DUET"
+                     , "mCSM-DUET"
                      , "FoldX"
                      , "DeepDDG"
                      , "Dynamut2"

scripts/plotting/plotting_thesis/katg/katg_ORandSNP_results.R

@@ -203,6 +203,14 @@ write.csv(bar_or, paste0(outdir_stats, "katg_OR_10.csv"))
 top10_or$position[top10_or$position%in%active_aa_pos]
 
 
+# maf
+bar_maf = bar_or[order(bar_or$maf_percent
+                      , bar_or$ligand_distance
+                      # bar_or$nca_dist
+                      , bar_or$interface_dist
+                      , decreasing = T), ]
+
+head(bar_maf)
 #########################################################
 # closest most sig
 bar_or_lig = bar_or[bar_or$ligand_distance<10,]