more plot files

scripts/plotting/plotting_thesis/gid/sensitivity_count_gid.R

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+#=========================
+# Count Sensitivity
+# Mutations and positions
+#=========================
+pos_colname_c ="position"
+
+sensP_df = merged_df3[,c("mutationinformation",
+                         #"position",
+                         pos_colname_c,
+                         "sensitivity")]
+
+head(sensP_df)
+table(sensP_df$sensitivity)
+
+#---------------
+# Total unique positions
+#----------------
+tot_mut_pos = length(unique(sensP_df[[pos_colname_c]]))
+cat("\nNo of Tot muts sites:", tot_mut_pos)
+
+# resistant mut pos
+sens_site_allR = sensP_df[[pos_colname_c]][sensP_df$sensitivity=="R"]
+sens_site_UR   = unique(sens_site_allR)
+length(sens_site_UR)
+
+# Sensitive mut pos
+sens_site_allS = sensP_df[[pos_colname_c]][sensP_df$sensitivity=="S"]
+sens_site_US = unique(sens_site_allS)
+length(sens_site_UR)
+
+#---------------
+# Common Sites
+#----------------
+common_pos = intersect(sens_site_UR,sens_site_US)
+site_Cc = length(common_pos)
+cat("\nNo of Common sites:", site_Cc
+    , "\nThese are:", common_pos)
+
+#---------------
+# Resistant muts
+#----------------
+site_R = sens_site_UR[!sens_site_UR%in%common_pos]
+site_Rc = length(site_R)
+
+if ( length(sens_site_allR) == table(sensP_df$sensitivity)[['R']] ){
+  cat("\nNo of R muts:", length(sens_site_allR) 
+      , "\nNo. of R sites:",site_Rc
+      , "\nThese are:", site_R
+)
+}
+
+#---------------
+# Sensitive muts
+#----------------
+site_S = sens_site_US[!sens_site_US%in%common_pos]
+site_Sc = length(site_S)
+
+if ( length(sens_site_allS) == table(sensP_df$sensitivity)[['S']] ){
+  cat("\nNo of S muts:", length(sens_site_allS) 
+      , "\nNo. of S sites:", site_Sc
+      , "\nThese are:", site_S)
+}
+
+#########################
+