diff --git a/boxplot_with_stats.R b/boxplot_with_stats.R
index c669c70..8fa217d 100755
--- a/boxplot_with_stats.R
+++ b/boxplot_with_stats.R
@@ -6,230 +6,37 @@ getwd()
 # TASK: boxplots at T1
 # FIXME: currently not rendering, problem with NAs for stats?
 ############################################################
-my_sample_type = "serum"
 #=============
 # Input
 #=============
-source("data_extraction_formatting.R")
+source("boxplot_linear.R")
 
-# check: adult variable and age variable discrepancy!
-metadata_all$mosaic[metadata_all$adult==1 & metadata_all$age<=18]
+mediators = levels(as.factor(lf_test$mediator))
 
-#=============
-# Output:
-#=============
-outfile_bp = paste0("boxplots_", my_sample_type, ".pdf")
-output_boxplot = paste0(outdir_plots, outfile_bp); output_boxplot
+plots <- list()
 
-#===============================
-# data assignment for plots
-#================================
-#wf_fp_npa = npa_wf[npa_wf$flustat == 1,]
-lf_fp_npa = npa_lf[npa_lf$flustat == 1,]
-lf_fp_npa$timepoint = paste0("t", lf_fp_npa$timepoint)
-lf_fp_npa$timepoint = as.factor(lf_fp_npa$timepoint)
-lf_fp_npa$obesity = as.factor(lf_fp_npa$obesity)
+for (i in mediators) {
+single=lf_test[lf_test$mediator==i,]
 
-table(lf_fp_npa$mediator)
-head(lf_fp_npa$value[lf_fp_npa$mediator == "vitd"])
-lf_fp_npa = lf_fp_npa[!lf_fp_npa$mediator == "vitd",]
+p2 = ggboxplot(single
+               , x = "timepoint"
+               , y = "value"
+               , color = "obesity"
+               , palette = c("#00BFC4", "#F8766D")
+               )
 
+stat_npa2 <- single %>%
+  group_by(timepoint, mediator) %>%
+  wilcox_test(value ~ obesity, paired = F) %>%
+  add_significance("p")
+stat_npa2
 
-#wf_fp_sam = samm_wf[samm_wf$flustat == 1,]
-lf_fp_sam = sam_lf[sam_lf$flustat == 1,]
-lf_fp_sam$timepoint = paste0("t", lf_fp_sam$timepoint)
-lf_fp_sam$timepoint = as.factor(lf_fp_sam$timepoint)
-lf_fp_sam$obesity = as.factor(lf_fp_sam$obesity)
+stat_npa2 <- stat_npa2 %>%
+  add_xy_position(x = "timepoint", dodge = 0.8)
 
-table(lf_fp_sam$mediator)
-head(lf_fp_sam$value[lf_fp_sam$mediator == "vitd"])
-lf_fp_sam = lf_fp_sam[!lf_fp_sam$mediator == "vitd",]
-
-
-#wf_fp_serum = serum_wf[serum_wf$flustat == 1,]
-lf_fp_serum = serum_lf[serum_lf$flustat == 1,]
-lf_fp_serum$timepoint = paste0("t", lf_fp_serum$timepoint)
-lf_fp_serum$timepoint = as.factor(lf_fp_serum$timepoint)
-lf_fp_serum$obesity = as.factor(lf_fp_serum$obesity)
-
-########################################################################
-cat("Output plots will be in:", output_boxplot)
-pdf(output_boxplot, width = 20, height = 15)
-
-#=======================================================================
-#                         NPA
-#=======================================================================
-if (is.factor(lf_fp_npa$timepoint) && is.factor(lf_fp_npa$timepoint)){
-  cat ("PASS: required groups are factors")
+p2 = p2 + stat_pvalue_manual(stat_npa2
+                             , label = "{p} {p.signif}"
+                             , hide.ns=T
+                             , tip.length = 0)
+plots[[i]] <- p2
 }
-#------------------------------------------
-title_npa_linear = "Boxplot: NPA (Linear)"
-#-----------------------------------------
-bxp_npa_linear <- ggboxplot(lf_fp_npa, 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() + 
-  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 = title_npa_linear
-       , x = ""
-       , y = "Levels")
-
-bxp_npa_linear
-
-#------------------------------------
-title_npa_log = "Boxplot: NPA (Log)"
-#-----------------------------------
-
-bxp_npa_log <- ggboxplot(lf_fp_npa, x = "timepoint", y = "value", 
-                         color = "obesity", palette = c("#00BFC4", "#F8766D")) +
-  facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = F)+
-  scale_y_log10() + 
-  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 = title_npa_log
-       , x = ""
-       , y = "Levels (Log)")
-
-bxp_npa_log
-
-#=======================================================================
-#                         SAM
-#=======================================================================
-if (is.factor(lf_fp_sam$timepoint) && is.factor(lf_fp_sam$timepoint)){
-  cat ("PASS: required groups are factors")
-}
-
-#------------------------------------------
-title_sam_linear = "Boxplot: sam (Linear)"
-#-----------------------------------------
-bxp_sam_linear <- ggboxplot(lf_fp_sam, 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() + 
-  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 = title_sam_linear
-       , x = ""
-       , y = "Levels")
-
-bxp_sam_linear
-
-#------------------------------------
-title_sam_log = "Boxplot: sam (Log)"
-#-----------------------------------
-
-bxp_sam_log <- ggboxplot(lf_fp_sam, 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() + 
-  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 = title_sam_log
-       , x = ""
-       , y = "Levels (Log)")
-
-bxp_sam_log
-
-#=======================================================================
-#                        SERUM
-#=======================================================================
-if (is.factor(lf_fp_serum$timepoint) && is.factor(lf_fp_serum$timepoint)){
-  cat ("PASS: required groups are factors")
-}
-
-table(lf_fp_serum$mediator)
-
-#------------------------------------------
-title_serum_linear = "Boxplot: serum (Linear)"
-#-----------------------------------------
-bxp_serum_linear <- ggboxplot(lf_fp_serum, 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() + 
-  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 = title_serum_linear
-       , x = ""
-       , y = "Levels")
-
-bxp_serum_linear
-
-#------------------------------------
-title_serum_log = "Boxplot: serum (Log)"
-#-----------------------------------
-
-bxp_serum_log <- ggboxplot(lf_fp_serum, 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() + 
-  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 = title_serum_log
-       , x = ""
-       , y = "Levels (Log)")
-
-bxp_serum_log 
-
-dev.off()
-#==========================================================================