diff --git a/boxplot.R b/boxplot.R
index e7d4e99..5d576ea 100644
--- a/boxplot.R
+++ b/boxplot.R
@@ -78,11 +78,6 @@ stat.test <- stat.test %>%
 bxp + stat_pvalue_manual(
   stat.test,  label = "p", tip.length = 0
 )
-
-
-
-
-
 ################################
 lf_test2 = lf[order(lf$mediator),] # 2 meds
 lf_test2 = lf_test2[1:798,]
@@ -98,7 +93,6 @@ stat.test <- lf_test2 %>%
 
 stat.test
 
-
 bxp <- ggboxplot(lf_test2, x = "timepoint", y = "value", 
                  color = "obesity", palette = c("#00BFC4", "#F8766D")) +
   facet_wrap(~mediator, scales = "free_y")
@@ -116,45 +110,62 @@ str(lf_comp)
 
 p2 = ggplot(lf_test_comp, aes(x = timepoint, y = value, fill = obesity ))  + 
   geom_boxplot(width = 0.5)
-p2 + stat_compare_means(comparisons = my_comparisons
-                         , method = "wilcox.test"
-                         , paired = F
-                         , label = "p.format") 
-
+p2 
 
 ########################################################################
 # Output plots as one pdf
 cat("Output plots will be in:", output_boxplot)
-pdf(output_boxplot, width=15, height=12)
+pdf(output_boxplot, width = 25, height = 15)
 
-y_value = "value"
-my_title1 = "Boxplots"
+#stats data
+str(lf)
+stat.test <- lf %>%
+  group_by(timepoint, mediator) %>%
+  wilcox_test(value ~ obesity, paired = F) %>%
+  #adjust_pvalue(method = "bonferroni") %>%
+  #add_significance("p.adj")
+  add_significance("p")
+stat.test
+
+bxp <- ggboxplot(lf, x = "timepoint", y = "value", 
+                 color = "obesity", palette = c("#00BFC4", "#F8766D")) +
+  facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = T)+
+  scale_y_log10()
+bxp
+
+bxp + stat.test <- stat.test %>%
+  add_xy_position(x = "timepoint", dodge = 0.8)
+
+bxp + stat_pvalue_manual(stat.test,  label = "p.signif", tip.length = 0)
 
-p1 = ggplot(lf, aes(x = factor(timepoint), y = eval(parse(text=y_value)), fill = factor(obesity) ))  + 
-  scale_fill_manual(values=c("#00BFC4", "#F8766D")) +
-  facet_wrap(~ mediator, nrow = 9, ncol = 4, scales = "free_y") + 
-  geom_boxplot(width = 0.5, outlier.colour = NA) +
-  #geom_point(position = position_jitterdodge(dodge.width=0.5)
-  #           , aes(colours = factor(obesity))) + 
-             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_text(size = 15)
-                   , axis.title.y = element_text(size = 15)
-                   , plot.title = element_text(size = 20, hjust = 0.5)
-                   , strip.text.x = element_text(size = 15, colour = "black")
-                   , legend.title = element_text(color = "black", size = 10)
-                   , legend.text = element_text(size = 15)
-                   , legend.direction = "vertical") +
-               labs(title = my_title1
-                    , x = ""
-                    , y = "Levels")+
-  stat_compare_means(comparisons = my_comparisons
-                     , method = "wilcox.test"
-                     , paired = F
-                     , label = "p.format") 
-#p1
-shift_legend2(p1)     
+dev.off()
+
+######output 
+
+# Output plots as one pdf
+cat("Output plots will be in:", output_boxplot)
+pdf(output_boxplot, width = 20, height = 15)
+my_title1 = "Boxplots: serum"
+
+bxp <- ggboxplot(lf, x = "timepoint", y = "value", 
+                 color = "obesity", palette = c("#00BFC4", "#F8766D")) +
+  facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = T)+
+  scale_y_log10()
+
+bxp + 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_text(size = 15)
+            , axis.title.y = element_text(size = 15)
+            , plot.title = element_text(size = 20, hjust = 0.5)
+            , strip.text.x = element_text(size = 15, colour = "black")
+            , legend.title = element_text(color = "black", size = 20)
+            , legend.text = element_text(size = 15)
+            , legend.direction = "horizontal") +
+  labs(title = my_title1
+       , x = ""
+       , y = "Levels (Log10)") 
+#shift_legend2(bxp)
 dev.off()