testing boxplot with stats

boxplot_with_stats.R

@@ -11,6 +11,10 @@ getwd()
 #=============
 source("boxplot_linear.R")
 
+#######################################################
+med_names = c("eotaxin3", "il12p70", "itac", "il13")
+lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,]
+
 mediators = levels(as.factor(lf_test$mediator))
 
 plots <- list()
@@ -18,12 +22,23 @@ plots <- list()
 for (i in mediators) {
 single=lf_test[lf_test$mediator==i,]
 
-p2 = ggboxplot(single
-               , x = "timepoint"
-               , y = "value"
-               , color = "obesity"
-               , palette = c("#00BFC4", "#F8766D")
-               )
+max_y = max(single$value, na.rm = T)
+cat("Plotting:", i, "max_y:", max_y, "\n")
+
+p2 = ggplot(single)+ geom_boxplot(aes(x = timepoint
+                     , y = value
+                     , color = obesity
+                    #, palette = c("#00BFC4", "#F8766D")
+                    ))+
+  theme(axis.text.x = element_text(size = 15)
+        , axis.text.y = element_text(size = 15
+                                     , angle = 0
+                                     , hjust = 1
+                                     , vjust = 0)
+        , axis.title.x = element_blank()
+        , axis.title.y = element_blank()
+        , legend.position = "none"
+        , plot.title = element_text(size = 20, hjust = 0.5))
 
 stat_npa2 <- single %>%
   group_by(timepoint, mediator) %>%
@@ -35,8 +50,12 @@ stat_npa2 <- stat_npa2 %>%
   add_xy_position(x = "timepoint", dodge = 0.8)
 
 p2 = p2 + stat_pvalue_manual(stat_npa2
+                             , y.position = max_y
                              , label = "{p} {p.signif}"
                              , hide.ns=T
-                             , tip.length = 0)
+                             , tip.length = 0)+
+  scale_y_continuous(expand = expansion(mult = c(0.05, 0.25)))
 plots[[i]] <- p2
 }
+
+cowplot::plot_grid(plotlist=plots, align = 'hv', ncol=2, nrow=2)