From 79b251047d2755c58ddb20fdd9c9c11d041ec0bd Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Thu, 25 Aug 2022 19:09:56 +0100
Subject: [PATCH] allow position_annotation to specify colours

---
 scripts/functions/position_annotation.R | 46 ++++++++++++++-----------
 1 file changed, 25 insertions(+), 21 deletions(-)

diff --git a/scripts/functions/position_annotation.R b/scripts/functions/position_annotation.R
index 068da6e..24b7edb 100644
--- a/scripts/functions/position_annotation.R
+++ b/scripts/functions/position_annotation.R
@@ -8,7 +8,11 @@ position_annotation=function(plot_df,
                              active_aa_pos=1:100,
                              aa_pos_lig1=1:100,
                              aa_pos_lig2=1:100,
-                             aa_pos_lig3=1:100
+                             aa_pos_lig3=1:100,
+                             drug_colour='green',
+                             lig1_colour='slategrey',
+                             lig2_colour='navyblue',
+                             lig3_colour='purple'
 )
 {
   x_ats = 12 
@@ -33,20 +37,20 @@ position_annotation=function(plot_df,
   
   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)
+                          "drug", 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)
+                           "lig1", 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)
+                           "lig2", 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)
+                            , "lig3", plot_df$col_bg3)
   
   # the call to generate_distance_colour_map should probably be
   # wherever the outer DF is built, and not here.
@@ -78,21 +82,21 @@ position_annotation=function(plot_df,
         #scale_x_discrete("Position", labels=factor(plot_df$position)) +
         scale_color_manual(values = c(
           "brown"="brown",
-          "green"="#00ff00",
+          "drug"=drug_colour,
           "transparent"="transparent",
-          "slategrey"="#2f4f4f",
-          "navyblue"="#000080",
-          "purple"="#a020f0"
+          "lig1"=lig1_colour,
+          "lig2"=lig2_colour,
+          "lig3"=lig3_colour
         ),
         #expand=c(0,0)
         ) +
         scale_fill_manual(values = c(
           "brown"="brown",
-          "green"="#00ff00",
+          "drug"=drug_colour,
           "transparent"="transparent",
-          "slategrey"="#2f4f4f",
-          "navyblue"="#000080",
-          "purple"="#a020f0"
+          "lig1"=lig1_colour,
+          "lig2"=lig2_colour,
+          "lig3"=lig3_colour
         ),
         #expand=c(0,0)
         ) +
@@ -117,21 +121,21 @@ position_annotation=function(plot_df,
         #scale_x_discrete("Position", labels=factor(plot_df$position)) +
         scale_color_manual(values = c(
           "brown"="brown",
-          "green"="#00ff00",
+          "drug"=drug_colour,
           "transparent"="transparent",
-          "slategrey"="#2f4f4f",
-          "navyblue"="#000080",
-          "purple"="#a020f0"
+          "lig1"=lig1_colour,
+          "lig2"=lig2_colour,
+          "lig3"=lig3_colour
         ),
         #expand=c(0,0)
         ) +
         scale_fill_manual(values = c(
           "brown"="brown",
-          "green"="#00ff00",
+          "drug"=drug_colour,
           "transparent"="transparent",
-          "slategrey"="#2f4f4f",
-          "navyblue"="#000080",
-          "purple"="#a020f0"
+          "lig1"=lig1_colour,
+          "lig2"=lig2_colour,
+          "lig3"=lig3_colour
         ),
         #expand=c(0,0)
         ) +