add a plot for the defence

haganjam · Nov 28, 2023 · 6fdb0d4 · 6fdb0d4
1 parent ee652bd
commit 6fdb0d4
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Showing 2 changed files with 43 additions and 2 deletions.
diff --git a/scripts/02_simulation/07_plot_RYE_values.R b/scripts/02_simulation/07_plot_RYE_values.R
@@ -74,7 +74,7 @@ p1 <-
 plot(p1)
 
 # export as a .svg file
-ggsave(filename = "figures/SI2_fig_S2.svg", p1,
+ggsave(filename = "figures/SI2_fig_S2.pdf", p1,
        unit = "cm", width = 20, height = 14)
 
 # check the range of RYEs for alpha = 3
@@ -83,4 +83,30 @@ dd_df %>%
   summarise(min = min(RYe),
             max = max(RYe))
 
+# plot a single one of these with alpha = 3
+p2 <- 
+  ggplot(data = dd_df |> dplyr::filter(alpha_3 == "yes"),
+       mapping = aes(x = Species, y = RYe, group = group)) +
+  geom_line(alpha = 0.1) +
+  scale_x_discrete(expand = c(0.05, 0.05)) +
+  scale_y_continuous(limits = c(0, 1)) +
+  xlab("Species") +
+  ylab(bquote("RY"[E])) +
+  theme_meta() +
+  theme(
+  panel.background = element_rect(fill='transparent'), #transparent panel bg
+  plot.background = element_rect(fill='transparent', color=NA), #transparent plot bg
+  panel.grid.major = element_blank(), #remove major gridlines
+  panel.grid.minor = element_blank(), #remove minor gridlines
+  legend.background = element_rect(fill='transparent'), #transparent legend bg
+  legend.box.background = element_rect(fill='transparent') #transparent legend panel
+)
+
+# export the figure for further modification
+ggsave(filename = "figures/def_fig_6.pdf", p2,
+       unit = "cm", width = 10, height = 8, bg = "transparent")
+
+
+
+
 ### END
diff --git a/scripts/03_empirical_analysis/02_case_study_2/03_data_analysis/08_analyse_BEF_effects.R b/scripts/03_empirical_analysis/02_case_study_2/03_data_analysis/08_analyse_BEF_effects.R
@@ -252,7 +252,7 @@ p123 <-
             rel_heights = c(1.5, 1, 2)) 
 plot(p123)
 
-ggsave(filename = "figures/MAIN_fig_4.svg", 
+ggsave(filename = "figures/MAIN_fig_4.pdf", 
        p123, units = "cm", width = 13, height = 18)
 
 # add a plot for the defence
@@ -347,6 +347,21 @@ p1 <-
   theme_meta()
 plot(p1)
 
+# export a plot for the defence
+p4_def <-
+  p1 +
+  theme(
+    panel.background = element_rect(fill='transparent'), #transparent panel bg
+    plot.background = element_rect(fill='transparent', color=NA), #transparent plot bg
+    panel.grid.major = element_blank(), #remove major gridlines
+    panel.grid.minor = element_blank(), #remove minor gridlines
+    legend.background = element_rect(fill='transparent'), #transparent legend bg
+    legend.box.background = element_rect(fill='transparent') #transparent legend panel
+  )
+
+ggsave(filename = "figures/def_fig_2.pdf", p4_def,
+       unit = "cm", width = 10, height = 8, bg = "transparent")
+
 slope_sum <- 
   lm_df %>%
   summarise(slope_m = mean(slope),