From c8f3ddf8926fdcb8cc4cc36e505320de05c167f9 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Sat, 13 Aug 2022 15:40:25 +0100
Subject: [PATCH] colour changes

---
 scripts/functions/bp_subcolours.R             |  2 ++
 .../functions/generate_distance_colour_map.R  |  9 ++++----
 scripts/functions/logoP_snp.R                 |  2 +-
 .../position_annotation.R                     | 15 ++++++------
 .../plotting_thesis/corr_plots_thesis.R       | 23 +++++++++++++++----
 5 files changed, 34 insertions(+), 17 deletions(-)
 rename scripts/{plotting => functions}/position_annotation.R (86%)

diff --git a/scripts/functions/bp_subcolours.R b/scripts/functions/bp_subcolours.R
index 24a6a58..29e79df 100755
--- a/scripts/functions/bp_subcolours.R
+++ b/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
diff --git a/scripts/functions/generate_distance_colour_map.R b/scripts/functions/generate_distance_colour_map.R
index 75a2d46..301dfb7 100644
--- a/scripts/functions/generate_distance_colour_map.R
+++ b/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
diff --git a/scripts/functions/logoP_snp.R b/scripts/functions/logoP_snp.R
index c492513..1046f45 100644
--- a/scripts/functions/logoP_snp.R
+++ b/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"
diff --git a/scripts/plotting/position_annotation.R b/scripts/functions/position_annotation.R
similarity index 86%
rename from scripts/plotting/position_annotation.R
rename to scripts/functions/position_annotation.R
index cd39cf1..706ddd4 100644
--- a/scripts/plotting/position_annotation.R
+++ b/scripts/functions/position_annotation.R
@@ -31,20 +31,21 @@ position_annotation=function(plot_df, bg="transparent"){
     scale_x_discrete("Position", labels=factor(plot_df$position)) +
     scale_color_manual(values = c(
       "brown"="brown",
-      "purple"="purple",
+      "green"="green",
       "transparent"="transparent",
-      "blue"="blue", "cyan"="cyan",
-      "cornflowerblue"="cornflowerblue"
+      "slategrey"="slategrey",
+      "navyblue"="navyblue",
+      "purple"="purple"
     ),
     expand=c(0,0)
     ) +
     scale_fill_manual(values = c(
       "brown"="brown",
-      "purple"="purple",
+      "green"="green",
       "transparent"="transparent",
-      "blue"="blue",
-      "cyan"="cyan",
-      "cornflowerblue"="cornflowerblue"
+      "slategrey"="slategrey",
+      "navyblue"="navyblue",
+      "purple"="purple"
     ),
     expand=c(0,0)
     ) +
diff --git a/scripts/plotting/plotting_thesis/corr_plots_thesis.R b/scripts/plotting/plotting_thesis/corr_plots_thesis.R
index 2681ecb..b9c6bf9 100644
--- a/scripts/plotting/plotting_thesis/corr_plots_thesis.R
+++ b/scripts/plotting/plotting_thesis/corr_plots_thesis.R
@@ -321,12 +321,25 @@ svg('/tmp/foo.svg', width=10, height=10, )
 
 corr_plotting_df = corr_df_ps
 
-ggpairs(corr_plotting_df, columns = 1:(ncol(corr_plotting_df)-1)
-        , upper = list(continuous = wrap('cor', method = "spearman"))
-        , aes(colour = factor(dst_mode), alpha = 0.5)
-        , title="correlogram with ggpairs()") + 
+ggpairs(corr_plotting_df, columns = 1:(ncol(corr_plotting_df)-1),
+        upper = list(continuous = wrap('cor',
+                                       method = "spearman",
+                                       title="ρ",
+                                       digits=2,
+                                       title_args=c(colour="black")
+        )
+        ),
+        lower = list(
+          continuous = wrap("points", alpha = 0.7, size=0.5),
+          combo     = wrap("dot", alpha = 0.7, size=0.5)
+        ),
+        aes(colour = factor(ifelse(corr_plotting_df$dst_mode==0, "S", "R")), alpha = 0.5),
+        title="Stability") +
   scale_colour_manual(values = c("red", "blue")) +
-  scale_fill_manual(values = c("red", "blue"))
+  scale_fill_manual(values = c("red", "blue")) + 
+  theme(
+    text = element_text(size=12, face="bold")
+  )
 
 dev.off()