From 8ddca4a8b1cf156a47a829a1e5e9032bc080fc79 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Thu, 17 Sep 2020 17:17:11 +0100
Subject: [PATCH] updated corr plots to show points with no colours

---
 scripts/plotting/corr_PS_LIG.R | 28 +++++++++++-----------------
 1 file changed, 11 insertions(+), 17 deletions(-)

diff --git a/scripts/plotting/corr_PS_LIG.R b/scripts/plotting/corr_PS_LIG.R
index d57ae26..0ea4a68 100644
--- a/scripts/plotting/corr_PS_LIG.R
+++ b/scripts/plotting/corr_PS_LIG.R
@@ -206,12 +206,13 @@ OutPlot1 = pairs.panels(my_corr_ps[1:(length(my_corr_ps)-1)]
              , rug = F
              , breaks = "Sturges"
              , show.points = T
-             , bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_ps$duet_outcome))]
-             , pch = 21
+             #, bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_ps$duet_outcome))] # can't use colour as duet and foldx are opposite
+             #, pch = 21 # for bg
+             , pch = 19
              , jitter = T
-             #, alpha = .05
+             , alpha = 1
              #, points(pch = 19, col = c("#f8766d", "#00bfc4"))
-             , cex = 3
+             , cex = 1.8
              , cex.axis = 2
              , cex.labels = 4
              , cex.cor = 1
@@ -237,12 +238,7 @@ OutPlot1_upper = my_pp(my_corr_ps[1:(length(my_corr_ps)-1)] # no lower panel
                  , stars = T
                  , rug = F
                  , breaks = "Sturges"
-                 , show.points = T
-                 , bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_ps$duet_outcome))]
-                 , pch = 21
-                 , jitter = T
-                 #, alpha = .05
-                 #, points(pch = 19, col = c("#f8766d", "#00bfc4"))
+                 , show.points = F
                  , cex = 3
                  , cex.axis = 1.6
                  , cex.labels = 4
@@ -322,12 +318,13 @@ OutPlot2  = pairs.panels(my_corr_lig[1:(length(my_corr_lig)-1)]
                          , rug = F
                          , breaks = "Sturges"
                          , show.points = T
-                         , bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_lig$ligand_outcome))]
-                         , pch = 21
+                         #, bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_lig$ligand_outcome))] # can't use colour as duet and foldx are opposite
+                         #, pch = 21 # for bg
+                         , pch = 19
                          , jitter = T
                          #, alpha = .05
                          #, points(pch = 19, col = c("#f8766d", "#00bfc4"))
-                         , cex = 3
+                         , cex = 2
                          , cex.axis = 2
                          , cex.labels = 4
                          , cex.cor = 1
@@ -353,10 +350,7 @@ OutPlot2_upper  = my_pp(my_corr_lig[1:(length(my_corr_lig)-1)]
                          , stars = T
                          , rug = F
                          , breaks = "Sturges"
-                         , show.points = T
-                         , bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_lig$ligand_outcome))]
-                         , pch = 21
-                         , jitter = T
+                         , show.points = F
                          #, alpha = .05
                          #, points(pch = 19, col = c("#f8766d", "#00bfc4"))
                          , cex = 3