From 3b77b4b611bf2a31f5cf32f078a16d1ffc2b77d6 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Wed, 24 Aug 2022 16:52:11 +0100
Subject: [PATCH] stuff

---
 scripts/functions/lf_bp.R          |  4 +-
 scripts/functions/wideP_consurf3.R | 60 +++++++++++++-----------------
 2 files changed, 28 insertions(+), 36 deletions(-)

diff --git a/scripts/functions/lf_bp.R b/scripts/functions/lf_bp.R
index 48b2162..4dcf365 100644
--- a/scripts/functions/lf_bp.R
+++ b/scripts/functions/lf_bp.R
@@ -73,7 +73,7 @@ lf_bp <- function(lf_df = lf_duet
                           )
                         )
                       )
-                    ) + ggplot2::scale_color_manual(values = consurf_bp_colours)  
+                    ) + ggplot2::scale_color_manual(values = consurf_colours)  
       
     } else {
     #Legend=factor(eval(parse(text = colour_categ)))
@@ -99,7 +99,7 @@ lf_bp <- function(lf_df = lf_duet
                       )
                     #, aes(colour = Legend)
                     ) +
-      ggplot2::scale_color_manual(values = consurf_bp_colours)
+      ggplot2::scale_color_manual(values = consurf_colours)
 
 
     }
diff --git a/scripts/functions/wideP_consurf3.R b/scripts/functions/wideP_consurf3.R
index 4053591..99eda2a 100644
--- a/scripts/functions/wideP_consurf3.R
+++ b/scripts/functions/wideP_consurf3.R
@@ -28,8 +28,8 @@ wideP_consurf3 <- function(plot_df
                                               , "1": "Variable"
                                               , "2", "3", "4", "5", "6", "7", "8"
                                               , "9": "Conserved")
-                           , panel_col      = "grey"
-                           , panel_col_fill = "grey"
+                           , panel_col      = "white"
+                           , panel_col_fill = "white"
                            
                            # axes title and label sizes
                            , x_axls = 12 # x-axis label size
@@ -70,6 +70,15 @@ wideP_consurf3 <- function(plot_df
                            , build_plot_df=FALSE
                            , debug=FALSE
 ){
+  anno_bar = position_annotation(
+    plot_df,
+    bg = panel_col,
+    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
+  )
   
   if(missing(point_colours)){
     temp_cols = colorRampPalette(c("seagreen", "sienna3"))(30)
@@ -171,7 +180,7 @@ wideP_consurf3 <- function(plot_df
                                  , y = yvar_colname
                                  , colour = sprintf("factor(%s)", yvar_colourN_colname)
   ))
-
+  
   
   #"if SPECIAL do SPECIAL THING, otherwise do NORMAL THING"
   if (plot_type == "bar"){
@@ -230,9 +239,9 @@ wideP_consurf3 <- function(plot_df
                                           , unit = unit_margin))+
     #guides(colour = guide_legend(title = "ConsurfXXXX")) +
     labs(x = NULL, y = NULL)
-    # labs(title = ptitle
-    #      , x = xlab
-    #      , y = ylab)
+  # labs(title = ptitle
+  #      , x = xlab
+  #      , y = ylab)
   
   #------------------
   #Extract legend1
@@ -242,7 +251,7 @@ wideP_consurf3 <- function(plot_df
                   , aes_string(
                     x = sprintf("factor(%s)"
                                 , xvar_colname))
-                  )
+  )
   g1_leg = g1_leg + geom_bar(); g1_leg
   g1_leg = g1_leg + geom_bar(aes_string(fill = sprintf("factor(%s)"
                                                        , yvar_colourN_colname))) 
@@ -254,41 +263,24 @@ wideP_consurf3 <- function(plot_df
   
   
   out = g1
+  
 
-    # x-axis: geom_tiles ~ active sites and others
+  # x-axis: geom_tiles ~ active sites and others
   if(annotate_active_sites){
-    aligned = align_plots(out,position_annotation(plot_df))
-    
+    #aligned = align_plots(out,position_annotation(plot_df))
     out=cowplot::plot_grid(
       out,
       NULL,
-      ggplot(plot_df, 
-             aes(x=factor(position), # THIS STUPID FUCKING FACTOR THING
-             )
-      ) +
-        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 = panel_col, colour=NA),
-              plot.margin = margin(t=0,b=0)) +
-        labs(x = NULL, y = NULL), #end of distance-heat-bar
-      NULL,
-      position_annotation(plot_df,
-                          bg = panel_col,
-                          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
-      ),
+      anno_bar,
       ncol=1,
       align='v',
-      axis='lr',
-      rel_heights = c(10,0,1,-0.1,1)
+      #axis='lr',
+      rel_heights = c(10,-0.1,1)
       
     )
-}
+  }
+  #### add the legends to the output ####
+  # ...which legends depend on whether the heat bar and position tiles are included 
   if (annotate_ligand_distance){
     cat('\nOutput: Plot + distance heat-bar + other stuff')
     legs = cowplot::plot_grid(legend1
@@ -314,4 +306,4 @@ wideP_consurf3 <- function(plot_df
   return(out2)
 }
 
-#wideP_consurf3(small_df3, point_colours = consurf_bp_colours)
+#wideP_consurf3(small_df3, point_colours = consurf_colours)