From 036cc14e40906b2135117ff61b8e6b0f2c0de669 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Tue, 14 Sep 2021 15:36:05 +0100
Subject: [PATCH] updated my_pairs_panel.R to make the dots coloured

---
 scripts/functions/my_pairs_panel.R | 44 ++++++++++++++++++++----------
 1 file changed, 30 insertions(+), 14 deletions(-)

diff --git a/scripts/functions/my_pairs_panel.R b/scripts/functions/my_pairs_panel.R
index 0c73192..eb0268a 100644
--- a/scripts/functions/my_pairs_panel.R
+++ b/scripts/functions/my_pairs_panel.R
@@ -1,24 +1,40 @@
-my_corr_pairs <- function (corr_data){
+my_corr_pairs <- function (corr_data_all
+                           , corr_data_range = 1:length(corr_data_all)
+                           , corr_method = "spearman" # other options: "pearson" or "kendall"
+                           , colour_categ_col = "mutation_info_labels"
+                           , categ_colour =  c("#E69F00", "#999999")
+                           , density_show = F
+                           , hist_col = "coral4"
+                           , dot_size = 1.6
+                           , ats = 1
+                           , corr_lab_size = 1
+                           , corr_value_size = 1) 
+  {
   
-  OutPlot_corr = pairs.panels(corr_data
-                              , method = "spearman" # correlation method
-                              , hist.col = "grey" ##00AFBB
-                              , density = TRUE  # show density plots
-                              , ellipses = F # show correlation ellipses
+  corr_data_df =  corr_data_all[corr_data_range]
+  my_bg = categ_colour[corr_data_all[[colour_categ_col]] ]
+
+  OutPlot_corr = pairs.panels(corr_data_df
+                              , method = corr_method
+                              , hist.col = hist_col
+                              , density = density_show  
+                              , ellipses = F 
+                              , smooth = F
                               , stars = T
                               , rug = F
                               , breaks = "Sturges"
                               , show.points = T
-                              #, bg = c("#f8766d", "#00bfc4")[unclass(factor(corr_ps$duet_outcome))] # foldx colours are reveresed
-                              #, pch = 21 # for bg
-                              , jitter = T
+                              #, bg = c("#f8766d", "#00bfc4")[unclass(factor(corr_data$duet_outcome))] # foldx colours are reveresed
+                              , bg = my_bg
+                              , pch = 21 
                               , alpha = 1
-                              , cex = 1.8
-                              , cex.axis = 2
-                              , cex.labels = 3.5
-                              , cex.cor = 1
-                              , smooth = F)
+                              , cex = dot_size
+                              , cex.axis = ats
+                              , cex.labels = corr_lab_size
+                              , cex.cor = corr_value_size
+                              )
   return(OutPlot_corr)
+  #return (my_bg)
   
 }