From e91d704929d3c3c5fb2c8bbbf415b77eac2b1603 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Fri, 9 Oct 2020 12:17:24 +0100
Subject: [PATCH] renamed other_plots.R to other_plots_combined.R and changing
 labels to capital letters for journal

---
 scripts/plotting/basic_barplots_combined.R    |  3 ++-
 .../plotting/lineage_dist_dm_om_combined_PS.R |  3 ++-
 scripts/plotting/logo_combined.R              |  3 ++-
 .../{other_plots.R => other_plots_combined.R} | 26 +++++++++++--------
 4 files changed, 21 insertions(+), 14 deletions(-)
 rename scripts/plotting/{other_plots.R => other_plots_combined.R} (93%)

diff --git a/scripts/plotting/basic_barplots_combined.R b/scripts/plotting/basic_barplots_combined.R
index 1a5e4ba..7fee2d7 100644
--- a/scripts/plotting/basic_barplots_combined.R
+++ b/scripts/plotting/basic_barplots_combined.R
@@ -29,7 +29,8 @@ svg(plot_basic_bp_combined_labelled , width = 12, height = 12 )
 
 bp_duet_combined = cowplot::plot_grid(OutPlot_count, OutPlot_pos_count
                                       , OutPlot_lig_count, OutPlot_lig_pos_count
-                                      , labels = c("(a)", "(b)", "(c)", "(d)")
+                                      #, labels = c("(a)", "(b)", "(c)", "(d)")
+                                      , labels = "AUTO"
                                       , label_size = 25)
 
 bp_duet_combined
diff --git a/scripts/plotting/lineage_dist_dm_om_combined_PS.R b/scripts/plotting/lineage_dist_dm_om_combined_PS.R
index 42950c6..fba6e18 100644
--- a/scripts/plotting/lineage_dist_dm_om_combined_PS.R
+++ b/scripts/plotting/lineage_dist_dm_om_combined_PS.R
@@ -372,7 +372,8 @@ plot_lineage_dist_combined_dm_om_L
 svg(plot_lineage_dist_combined_dm_om_L, width = 12, height = 6)
 
 OutPlot2 = cowplot::plot_grid(p1, p2
-                              , labels = c("(a)", "(b)")
+                              #, labels = c("(a)", "(b)")
+                              , labels = "AUTO"
                               #, label_x = -0.045, label_y = 0.92
                               #, hjust = -0.7, vjust = -0.5
                               #, align = "h"
diff --git a/scripts/plotting/logo_combined.R b/scripts/plotting/logo_combined.R
index 387f1ca..24df20e 100644
--- a/scripts/plotting/logo_combined.R
+++ b/scripts/plotting/logo_combined.R
@@ -269,7 +269,8 @@ svg(plot_logo_combined_labelled, width = 25, height = 10)
 OutPlot2 = cowplot::plot_grid(logo_or, p1, p3
                               , nrow = 3
                               , align = "hv"
-                              , labels = c("(a)","(b)", "(c)")
+                              #, labels = c("(a)","(b)", "(c)")
+                              , labels = "AUTO"
                               , rel_heights = c(3/8, 3/8, 1.5/8)
                               , rel_widths = c(0.85, 1, 1)
                               , label_size = 25)
diff --git a/scripts/plotting/other_plots.R b/scripts/plotting/other_plots_combined.R
similarity index 93%
rename from scripts/plotting/other_plots.R
rename to scripts/plotting/other_plots_combined.R
index ba5409a..ca0632b 100644
--- a/scripts/plotting/other_plots.R
+++ b/scripts/plotting/other_plots_combined.R
@@ -24,12 +24,11 @@ plot_dr_other_combined  =  paste0(plotdir,"/", dr_other_combined)
 dr_other_combined_labelled = "dr_other_muts_labelled.svg"
 plot_dr_other_combined_labelled  =  paste0(plotdir,"/", dr_other_combined_labelled)
 
+#dr_other_foldx = "dr_other_muts_foldx.svg"
+#plot_dr_other_foldx  =  paste0(plotdir,"/", dr_other_foldx)
 
-dr_other_foldx = "dr_other_muts_foldx.svg"
-plot_dr_other_foldx  =  paste0(plotdir,"/", dr_other_foldx)
-
-point_legend = "point_legend.svg"
-plot_point_legend  =  paste0(plotdir,"/", point_legend)
+#point_legend = "point_legend.svg"
+#plot_point_legend  =  paste0(plotdir,"/", point_legend)
 ########################################################################
 #               end of data extraction and cleaning for plots          #
 ########################################################################
@@ -218,7 +217,9 @@ svg(plot_dr_other_combined, width = 24, height = 12)
 
 # first combine fold and lig plots (2 and 3)
 c1 = cowplot::plot_grid(p2, p3
-                        , labels = c("(b)", "(c)")
+                        #, labels = c("(b)", "(c)")
+                        , labels = c("B", "C")
+                        , hjust = -2
                         , label_size = 25
                         , nrow = 1
                         , rel_widths = c(1/6, 5/6))
@@ -237,7 +238,10 @@ plot_dr_other_combined_labelled
 
 Outplot_labelled = cowplot::plot_grid(p1, c1
                         , nrow = 2
-                        , labels = c("(a)", "", "")
+                        #, labels = c("(a)", "", "")
+                        , labels = c("A", "", "")
+                        , hjust = -2
+                        #, vjust = 0
                         , label_size = 25)
 
 print(Outplot_labelled)
@@ -248,10 +252,10 @@ dev.off()
 #---------
 # plot 3: legend
 #---------
-svg(plot_point_legend, width = 6, height = 7)
-OutPlot3 =  legend
-print(OutPlot3)
-dev.off()
+#svg(plot_point_legend, width = 6, height = 7)
+#OutPlot3 =  legend
+#print(OutPlot3)
+#dev.off()