colour changes

scripts/functions/bp_subcolours.R

@@ -124,6 +124,8 @@ bp_stability_hmap <- function(plot_df = merged_df3
         , axis.title.y = element_text(size = my_yaxts )
         , plot.title = element_text(size = my_pts
                                     , hjust = 0.5)
+        , panel.grid = element_blank()
+        , panel.background = element_rect(fill = "transparent", colour=NA)
         ) +
       
       labs(title = p_title

scripts/functions/generate_distance_colour_map.R

@@ -2,7 +2,8 @@
 generate_distance_colour_map = function(plot_df,
                                         xvar_colname = "position",
                                         lig_dist_colname = "ligand_distance",
-                                        lig_dist_colours = c("green", "yellow", "orange", "red"),
+                                        #lig_dist_colours = c("green", "yellow", "orange", "red"),
+                                        lig_dist_colours = c("tan", "black"),
                                         debug = TRUE
 )
 {
@@ -74,9 +75,9 @@ generate_distance_legend = function(plot_df,
       geom_tile(aes(fill = .data[[lig_dist_colname]])
                 , colour = "white") +
       scale_fill_gradient2(midpoint = lig_mean
-                           , low  = "green"
-                           , mid  = "yellow"
-                           , high = "red"
+                           , low  = "tan"
+                           , mid  = "grey50"
+                           , high = "black"
                            , breaks = labels
                            , limits = c(lig_min, lig_max)
                            , labels = labelsD

scripts/functions/logoP_snp.R

@@ -201,7 +201,7 @@ LogoPlotSnps <- function(plot_df
     cat('\nSelected colour scheme:', my_logo_col
         , "\nUsing grey theme")
     
-    theme_bgc = "grey"
+    theme_bgc = "white"
     xfont_bgc  = "black"
     yfont_bgc  = "black"
     xtt_col    = "black"

scripts/functions/position_annotation.R

@@ -0,0 +1,60 @@
+# 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"){
+  x_ats = 12 
+  x_tangle = 90 
+  x_tts = 20 
+  y_tts = 23
+  xtt_col    = "black"
+  ytt_col    = "black"
+  leg_dir = "horizontal" 
+  leg_ts = 15 
+  leg_tts = 16
+  leg_pos = "none" 
+  
+  #plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
+  
+  ggplot(plot_df, 
+         aes(x=factor(position), # THIS STUPID FUCKING FACTOR THING
+         )
+  ) +
+    geom_tile(aes(y=0, fill= bg_all, colour = bg_all)
+    ) +
+    geom_tile(aes(y=1, fill= col_bg1, colour = col_bg1)
+    ) +
+    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)
+}
+