oops!

scripts/functions/position_annotation.R

@@ -1,7 +1,15 @@
 # position_annotation takes a Data Frame (df) and returns a ggplot object.
 # 
 # This plots position tiles for the (up to) three ligands as well as drug
-position_annotation=function(plot_df, bg="transparent"){
+position_annotation=function(plot_df,
+                             bg="transparent",
+                             aa_pos_drug=1:100,
+                             active_aa_pos=1:100,
+                             aa_pos_lig1=1:100,
+                             aa_pos_lig2=1:100,
+                             aa_pos_lig3=1:100
+)
+{
   x_ats = 12 
   x_tangle = 90 
   x_tts = 20 
@@ -13,48 +21,117 @@ position_annotation=function(plot_df, bg="transparent"){
   leg_tts = 16
   leg_pos = "none" 
   
+  # plot_df=plot_df[order(plot_df$ligand_distance),]
+  # 
+  # plot_df$position = factor(plot_df$position)
   #plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
+  # plot_df$col_aa = ifelse(plot_df[["position"]]%in%active_aa_pos,
+  #                         "brown", "transparent")
+  plot_df$col_aa = ifelse(plot_df[["position"]]%in%active_aa_pos,
+                          "transparent", "transparent")
   
-  ggplot(plot_df, 
-         aes(x=factor(position), # THIS STUPID FUCKING FACTOR THING
-         )
-  ) +
-    geom_tile(aes(y=0, fill= bg_all, colour = bg_all)
+  plot_df$bg_all = plot_df$col_aa
+  plot_df$bg_all = ifelse(plot_df[["position"]]%in%aa_pos_drug,
+                          "green", plot_df$bg_all)
+  
+  plot_df$col_bg1 = plot_df$bg_all
+  plot_df$col_bg1 = ifelse(plot_df[["position"]]%in%aa_pos_lig1,
+                           "slategrey", plot_df$col_bg1)
+  
+  plot_df$col_bg2 = plot_df$col_bg1
+  plot_df$col_bg2 = ifelse(plot_df[["position"]]%in%aa_pos_lig2,
+                           "navyblue", plot_df$col_bg2)
+  
+  
+  plot_df$col_bg3 = plot_df$col_bg2
+  plot_df$col_bg3 =  ifelse(plot_df[["position"]]%in%aa_pos_lig3
+                            , "purple", plot_df$col_bg3)
+  
+  plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
+  
+  cowplot::plot_grid(
+    ggplot(plot_df, 
+           aes(x=factor(position), # THIS STUPID FUCKING FACTOR THING
+           )
     ) +
-    geom_tile(aes(y=1, fill= col_bg1, colour = col_bg1)
+      geom_tile(aes(y=0), 
+                fill=plot_df$ligD_colours) +
+      #scale_x_discrete("Position", labels=factor(plot_df$position)) +
+      #theme_nothing() +
+      theme(plot.background = element_rect(fill = "transparent", colour=NA),
+            plot.margin = margin(t=0,b=0),
+            axis.ticks.x = element_blank(),
+            axis.ticks.y = element_blank(),
+            axis.text.y = element_blank(),
+            panel.grid = element_blank(),
+            panel.background = element_rect(fill = "transparent", colour=NA),
+      ) +
+      labs(x = NULL, y = NULL), #end of distance-heat-bar
+    #NULL,
+    ggplot(plot_df, 
+           aes(x=factor(position), # THIS STUPID FUCKING FACTOR THING
+               #reorder(ligand_distance)
+           )
     ) +
-    geom_tile(aes(y=2, fill= col_bg2, colour = col_bg2)
-    ) +
-    geom_tile(aes(y=3, fill= col_bg3, colour = col_bg3)
-    ) +
-    
-    scale_x_discrete("Position", labels=factor(plot_df$position)) +
-    scale_color_manual(values = c(
-      "brown"="brown",
-      "green"="green",
-      "transparent"="transparent",
-      "slategrey"="slategrey",
-      "navyblue"="navyblue",
-      "purple"="purple"
-    ),
-    expand=c(0,0)
-    ) +
-    scale_fill_manual(values = c(
-      "brown"="brown",
-      "green"="green",
-      "transparent"="transparent",
-      "slategrey"="slategrey",
-      "navyblue"="navyblue",
-      "purple"="purple"
-    ),
-    expand=c(0,0)
-    ) +
-    #scale_x_continuous(expand=c(0,0)) +
-    #scale_y_continuous(expand=c(0,0)) +
-    theme_nothing() +
-    
-    theme(plot.background = element_rect(fill = bg, colour=NA),
-          plot.margin = margin(t=0,b=0)) +
-    labs(x = NULL, y = NULL)
+      # geom_tile(aes(y = 0, fill = col_aa, colour = col_aa)
+      # ) +
+      geom_tile(aes(y = 1, fill = bg_all, colour = bg_all)
+      ) +
+      geom_tile(aes(y = 2, fill = col_bg1, colour = col_bg1)
+      ) +
+      geom_tile(aes(y = 3, fill = col_bg2, colour = col_bg2)
+      ) +
+      geom_tile(aes(y = 4, fill = col_bg3, colour = col_bg3)
+      ) +
+      
+      #scale_x_discrete("Position", labels=factor(plot_df$position)) +
+      scale_color_manual(values = c(
+        "brown"="brown",
+        "green"="#00ff00",
+        "transparent"="transparent",
+        "slategrey"="#2f4f4f",
+        "navyblue"="#000080",
+        "purple"="#a020f0"
+      ),
+      expand=c(0,0)
+      ) +
+      scale_fill_manual(values = c(
+        "brown"="brown",
+        "green"="#00ff00",
+        "transparent"="transparent",
+        "slategrey"="#2f4f4f",
+        "navyblue"="#000080",
+        "purple"="#a020f0"
+      ),
+      expand=c(0,0)
+      ) +
+      #scale_x_continuous(expand=c(0,0)) +
+      #scale_y_continuous(expand=c(0,0)) +
+      theme_nothing() +
+      
+      theme(plot.background = element_rect(fill = bg, colour=NA),
+            plot.margin = margin(t=0,b=0)) +
+      labs(x = NULL, y = NULL),
+    ncol=1,
+    rel_heights = c(1,
+                    #-0.1,
+                    1)
+  )
 }
 
+position_annotation(merged_df3,
+                    aa_pos_drug=aa_pos_drug,
+                    active_aa_pos=active_aa_pos,
+                    aa_pos_lig1=aa_pos_lig1,
+                    aa_pos_lig2=aa_pos_lig2,
+                    aa_pos_lig3=aa_pos_lig3
+)
+# 
+# # proof that you can use this function to pass arbitrary lists of numbers :-)
+# position_annotation(merged_df3,
+#                     aa_pos_drug=1:1000,
+#                     active_aa_pos=1:1000,
+#                     aa_pos_lig1=1:1000,
+#                     aa_pos_lig2=1:1000,
+#                     aa_pos_lig3=1:1000
+# )