From 9784cba232bc8523387401d713a07166d920f3ea Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Tue, 6 Oct 2020 18:15:50 +0100
Subject: [PATCH] generated labelled ps_plots_combined.R and capital "P" for
 position in barplots coloured aa for Lig

---
 scripts/plotting/barplots_subcolours_aa_LIG.R |  8 ++--
 scripts/plotting/ps_plots_combined.R          | 37 ++++++++++++++-----
 2 files changed, 31 insertions(+), 14 deletions(-)

diff --git a/scripts/plotting/barplots_subcolours_aa_LIG.R b/scripts/plotting/barplots_subcolours_aa_LIG.R
index f00466b..9f7a70f 100755
--- a/scripts/plotting/barplots_subcolours_aa_LIG.R
+++ b/scripts/plotting/barplots_subcolours_aa_LIG.R
@@ -20,7 +20,7 @@ library(ggplot2)
 library(data.table)
 source("barplot_colour_function.R")
 #source("subcols_axis.R")
-source("subcols_axis_PS.R")
+source("subcols_axis.R")
 
 # should return the following dfs, directories and variables
 # mut_pos_cols
@@ -218,7 +218,7 @@ svg(plot_bp_aa_subcols_ligand, width = 26, height = 4)
 
 g = ggplot(df, aes(factor(position, ordered = T)))
 
-outPlot = g + 
+OutPlot = g + 
   coord_cartesian(xlim = c(1, my_xlim)
                   #, ylim = c(0, 6)
                   , ylim = c(0, max(snp_count))
@@ -249,10 +249,10 @@ outPlot = g +
          , axis.ticks.x = element_blank()) +
   labs(title = ""
        #title = my_title
-       , x = "position"
+       , x = "Position"
        , y = "Frequency")
 
-print(outPlot)
+print(OutPlot)
 dev.off()
 
 #!!!!!!!!!!!!!!!!
diff --git a/scripts/plotting/ps_plots_combined.R b/scripts/plotting/ps_plots_combined.R
index afcdc25..d62d8ee 100644
--- a/scripts/plotting/ps_plots_combined.R
+++ b/scripts/plotting/ps_plots_combined.R
@@ -219,6 +219,7 @@ p2 = g2 +
            , colour = "black"
            , fill = "lightgray"
            , stat = "identity") +
+  scale_y_continuous(limits = c(0, 450))+
   theme(axis.text.x = element_blank()
          , axis.text.y = element_text(size = my_ats
                                       , angle = 0
@@ -235,17 +236,33 @@ p2
 ########################################################################
 #               			end of DUET barplots         			               #
 ########################################################################
-#=======
-# output
-#=======
-ps_plots_combined = "af_or_combined_PS.svg"
-plot_ps_plots_combined  =  paste0(plotdir,"/", ps_plots_combined )
+#============================
+# combined plot 1: UNlabelled
+#============================
+ps_combined = "af_or_combined_PS.svg"
+plot_ps_combined  =  paste0(plotdir,"/", ps_combined)
+cat("combined plot Unlabelled:", plot_ps_combined)
 
-svg(plot_ps_plots_combined , width = 26, height = 12)
-
-#theme_set(theme_gray()) # to preserve default theme
-printFile = cowplot::plot_grid(p1, p2, p3
+svg(plot_ps_combined , width = 26, height = 12)
+OutPlot_combined = cowplot::plot_grid(p1, p2, p3
                             , ncol = 1
                             , align = 'v')
-printFile
+OutPlot_combined
 dev.off()
+
+#============================
+# combined plot 2: labelled
+#============================
+ps_combined_labelled = "af_or_combined_PS_labelled.svg"
+plot_ps_combined_labelled =  paste0(plotdir,"/", ps_combined_labelled)
+cat("combined plot Labelled:", plot_ps_combined_labelled)
+
+svg(plot_ps_combined_labelled , width = 26, height = 12)
+OutPlot_combined_labelled = cowplot::plot_grid(p1, p2, p3
+                                       , ncol = 1
+                                       , labels = c("(a)", "(b)", "(c)")
+                                       , label_size = 21
+                                       , align = 'v'
+                                       , hjust = -0.4)
+OutPlot_combined_labelled
+dev.off()
\ No newline at end of file