From 40e4ddd70ac035726b4c8ab36951999d3ee3c37f Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Thu, 17 Sep 2020 20:00:34 +0100
Subject: [PATCH] minor tweaks in logo and corr plots

---
 scripts/plotting/corr_PS_LIG.R        |  9 +++++++--
 scripts/plotting/logo_multiple_muts.R |  1 -
 scripts/plotting/logo_plot.R          | 23 +++++++++++++++++------
 3 files changed, 24 insertions(+), 9 deletions(-)

diff --git a/scripts/plotting/corr_PS_LIG.R b/scripts/plotting/corr_PS_LIG.R
index 0ea4a68..b6ea1d7 100644
--- a/scripts/plotting/corr_PS_LIG.R
+++ b/scripts/plotting/corr_PS_LIG.R
@@ -59,6 +59,9 @@ cat(paste0("Variables imported:"
 corr_ps = "corr_PS.svg"
 plot_corr_ps =  paste0(plotdir,"/", corr_ps)
 
+corr_ps_duet_col = "corr_PS_duet_coloured.svg"
+plot_corr_ps_duet_col =  paste0(plotdir,"/", corr_ps_duet_col)
+
 corr_upper_ps = "corr_upper_PS.svg"
 plot_corr_upper_ps = paste0(plotdir,"/", corr_upper_ps)
 
@@ -193,10 +196,12 @@ head(my_corr_ps)
 #---------------------------------------
 # generate corr PS plot 1: both panels
 #---------------------------------------
-
-cat("Corr plot PS:", plot_corr_ps)
+cat("Corr plot PS DUET with coloured dots:", plot_corr_ps)
 svg(plot_corr_ps, width = 15, height = 15)
 
+#cat("Corr plot PS DUET with coloured dots:",plot_corr_ps_duet_col)
+#svg(plot_corr_ps_duet_col, width = 15, height = 15)
+
 OutPlot1 = pairs.panels(my_corr_ps[1:(length(my_corr_ps)-1)]
              , method = "spearman" # correlation method
              , hist.col = "grey" ##00AFBB
diff --git a/scripts/plotting/logo_multiple_muts.R b/scripts/plotting/logo_multiple_muts.R
index f6d5344..fb9ec63 100644
--- a/scripts/plotting/logo_multiple_muts.R
+++ b/scripts/plotting/logo_multiple_muts.R
@@ -173,7 +173,6 @@ p3 = p2 +
 
 p3
 
-
 # Now combine using cowplot, which ensures the plots are aligned
 suppressMessages( require(cowplot) )
 
diff --git a/scripts/plotting/logo_plot.R b/scripts/plotting/logo_plot.R
index a96cdb9..7294d8e 100644
--- a/scripts/plotting/logo_plot.R
+++ b/scripts/plotting/logo_plot.R
@@ -116,6 +116,7 @@ wide_df_or <- logo_data_or %>% spread(position, or_mychisq, fill = 0.0)
 wide_df_or = as.matrix(wide_df_or)
 rownames(wide_df_or) = wide_df_or[,1]
 wide_df_or = wide_df_or[,-1]
+str(wide_df_or)
 
 position_or = as.numeric(colnames(wide_df_or))
 
@@ -124,22 +125,32 @@ position_or = as.numeric(colnames(wide_df_or))
 #============================================  
 # custom height (OR) logo plot: yayy works
 
-ggseqlogo(wide_df_or, method="custom", seq_type="aa") + ylab("my custom height") +
-    theme(legend.position = "bottom"
-          , axis.text.x = element_text(size = 11
+cat("Logo plot with OR as y axis:", plot_logo_plot)
+svg(plot_logo_plot, width = 30 , height = 6)
+
+logo_or = ggseqlogo(wide_df_or, method="custom", seq_type="aa") + ylab("my custom height") +
+    theme( axis.text.x = element_text(size = 16
                                        , angle = 90
                                        , hjust = 1
                                        , vjust = 0.4)
-          , axis.text.y = element_text(size = 15
+          , axis.text.y = element_text(size = 22
                                        , angle = 0
                                        , hjust = 1
-                                       , vjust = 0))+
-    scale_x_discrete("Position"
+                                       , vjust = 0)
+          , axis.title.y = element_text(size = 25)
+          , axis.title.x = element_text(size = 20)
+          #, legend.position = "bottom") + 
+          , legend.position = "none")+
+          #, legend.text = element_text(size = 15)
+          #, legend.title = element_text(size = 15))+
+      scale_x_discrete("Position"
                      #, breaks
                      , labels = position_or
                      , limits = factor(1:length(position_or))) +
   ylab("Odds Ratio")
   
+print(logo_or)
+dev.off()
 #%% end of logo plot with OR as height
 
 #=======================================================================