added stat_bp_stability.R which needs to be a function for generating stat plots

2021-08-26 16:37:56 +01:00 · 2021-08-26 16:37:56 +01:00 · 6e01ef22c0
commit 6e01ef22c0
parent 6d9412d232
1 changed files with 51 additions and 0 deletions
--- a/scripts/functions/stat_bp_stability.R
+++ b/scripts/functions/stat_bp_stability.R
@ -0,0 +1,51 @@
+my_stat_ps = compare_means(param_value~mutation_info, group.by = "param_type"
+                           , data = df_lf_ps,  paired = FALSE, p.adjust.method = "BH")
+
+y_value = "param_value"
+
+stat_bp_mut <- function(df
+                        , x_bp_cateog = "mutation_info"
+                        , y_var = "param_value"
+                        , facet_var = "param_type"
+                        , scales = "free_y"
+                        , title = ""
+                        , col_categ = "duet_outcome"
+                        , grp_comp = "my_comparisons"
+                        , stat_method = "wilcox.test"
+                        , my_paired = FALSE
+                        #, stat_label = "p.format")
+                        , stat_label = "p.signif" )
+
+p1 = ggplot(df_lf_ps, aes(x = mutation_info
+                          , y = eval(parse(text = y_value)) ))  + 
+  facet_wrap(~ param_type
+             , nrow = 1
+             , scales = "free_y") + 
+  geom_boxplot(fill = "white", outlier.colour = NA
+               #, position = position_dodge(width = 0.9)
+               , width = 0.2) +
+  geom_point(position = position_jitterdodge(dodge.width=0.01)
+             , alpha = 0.5
+             , show.legend = FALSE
+             , aes(colour = factor(duet_outcome))) +
+  theme(axis.text.x = element_text(size = my_ats)
+        , axis.text.y = element_text(size = my_ats
+                                     , angle = 0
+                                     , hjust = 1
+                                     , vjust = 0)
+        , axis.title.x = element_text(size = my_ats)
+        , axis.title.y = element_text(size = my_ats)
+        , plot.title = element_text(size = my_pts , hjust = 0.5, colour = "black", face = "bold")
+        , strip.background = element_rect(fill = "khaki2")
+        , strip.text.x = element_text(size = my_fls, colour = "black")
+        , legend.title = element_text(color = "black", size = my_als)
+        , legend.text = element_text(size = my_ats)
+        , legend.direction = "vertical") +
+  labs(title = "DUET"
+       , x = ""
+       , y = "")+ 
+  stat_compare_means(comparisons = my_comparisons
+                     , method = "wilcox.test"
+                     , paired = FALSE
+                     #, label = "p.format")
+                     , label = "p.signif")