#!/usr/bin/Rscript   
getwd()
setwd("~/git/mosaic_2020/")
getwd()
############################################################
# TASK: boxplots at T1
# FIXME: currently not rendering, problem with NAs for stats?
############################################################
#=============
# Input
#=============
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()

for (i in mediators) {
single=lf_test[lf_test$mediator==i,]

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) %>%
  wilcox_test(value ~ obesity, paired = F) %>%
  add_significance("p")
stat_npa2

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)+
  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)