From 4ce2087224e54f6e629be386b52dfa8d8cd6a25f Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Mon, 8 Aug 2022 16:48:40 +0100
Subject: [PATCH] various changes

---
 scripts/functions/bp_subcolours.R                |  4 ++--
 scripts/functions/generate_distance_colour_map.R |  1 -
 scripts/functions/wideP_consurf.R                | 12 +++++++-----
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/scripts/functions/bp_subcolours.R b/scripts/functions/bp_subcolours.R
index 5adc071..9dc7607 100755
--- a/scripts/functions/bp_subcolours.R
+++ b/scripts/functions/bp_subcolours.R
@@ -68,7 +68,7 @@ bp_stability_hmap <- function(plotdf = merged_df3
   # Build data with colours
   # ~ ligand distance
   #=========================
-  plotdf = generate_distance_colour_map(plotdf, yvar_colname = stability_colname, debug=TRUE)
+  plotdf = generate_distance_colour_map(plotdf, debug=TRUE)
   
   # order the df by position and ensure it is a factor
   plotdf = plotdf[order(plotdf[[xvar_colname]]), ]
@@ -131,7 +131,7 @@ bp_stability_hmap <- function(plotdf = merged_df3
       labs(title = p_title
            , x = my_xlab
            , y = my_ylab),
-    generate_distance_legend(plotdf, yvar_colname = stability_colname),
+    generate_distance_legend(plotdf),
     ncol = 2,
     #align = "hv",
     rel_widths = c(9/10, 0.4/10)
diff --git a/scripts/functions/generate_distance_colour_map.R b/scripts/functions/generate_distance_colour_map.R
index 8110676..75a2d46 100644
--- a/scripts/functions/generate_distance_colour_map.R
+++ b/scripts/functions/generate_distance_colour_map.R
@@ -55,7 +55,6 @@ generate_distance_colour_map = function(plot_df,
 }
 
 generate_distance_legend = function(plot_df,
-                                    yvar_colname,
                                     xvar_colname = 'position',
                                     lig_dist_colname = "ligand_distance",
                                     legend_title = "Ligand\nDistance"
diff --git a/scripts/functions/wideP_consurf.R b/scripts/functions/wideP_consurf.R
index 28fc2de..31c7ab0 100644
--- a/scripts/functions/wideP_consurf.R
+++ b/scripts/functions/wideP_consurf.R
@@ -13,6 +13,11 @@
 # input args
 #==========================================================
 wideP_consurf2 <- function(plot_df
+                           , aa_pos_drug = NULL
+                           , aa_pos_lig1 = NULL
+                           , aa_pos_lig2 = NULL
+                           , aa_pos_lig3 = NULL
+                           
                            , xvar_colname = "position"
                            , yvar_colname = "consurf_score"
                            , yvar_colourN_colname = "consurf_colour_rev" # num from 0-1
@@ -66,20 +71,17 @@ wideP_consurf2 <- function(plot_df
                            
                            # Custom 3: x-axis: geom tiles ~ active sites and ligand
                            , annotate_active_sites = F
-                           , aa_pos_drug = aa_pos_drug
+                           
                            , drug_aa_colour = "purple"
                            , active_aa_pos = NULL
                            , active_aa_colour = "brown"
                            
-                           , aa_pos_lig1 = NULL
                            , aa_colour_lig1 = "blue"
                            , tpos1 = 0
                            
-                           , aa_pos_lig2 = NULL
                            , aa_colour_lig2 =  "cyan"
                            , tpos2 = 0
                            
-                           , aa_pos_lig3 = NULL
                            , aa_colour_lig3 =  "cornflowerblue"
                            , tpos3 = 0
                            
@@ -487,7 +489,7 @@ wideP_consurf2 <- function(plot_df
   if (annotate_ligand_distance){
     cat('\nOutput: Plot + distance heat-bar + other stuff')
     legs = cowplot::plot_grid(legend1
-                              , generate_distance_legend(plot_df, yvar_colname = yvar_colname)
+                              , generate_distance_legend(plot_df)
                               , ncol = 1
                               , align = "hv"
                               , rel_heights = c(2/4,3/4))