#!/usr/bin/Rscript   
getwd()
setwd("~/git/mosaic_2020/")
getwd()
############################################################
# TASK: boxplots at T1
# FIXME: currently not rendering, problem with NAs for stats?
############################################################
doMyPlots <- function(x, title  = "TEST") {
    mediators = levels(as.factor(x$mediator))
    
    plots <- list()
    
    for (i in mediators) {
      cat("Plotting:", i, "\n")
      single=x[x$mediator==i,]
      
      max_y = max(single$value, na.rm = T)
      cat("Plotting:", i, "max_y:", max_y, "\n")
      
      # boxplot
      p2 = ggboxplot(single
                     , x = "timepoint"
                     , y = "value"
                     , color = "obesity"
                     , palette = c("#00BFC4", "#F8766D"))
        
      p2 = p2 +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_
                     , 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
             , x = ""
             , y = "Levels")
      
      # stats
      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)
      
      # add stats to boxplot
      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
    }
    return(plots)

  }

###############################################################
#============
# test
#============
source("boxplot_linear.R")

#=============
# Output:
#=============
outfile_bp = paste0("boxplots_TEST_stats_all", ".pdf")
output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats

pdf(output_boxplot_stats, width=32, height=18)

med_names = c("eotaxin3", "il12p70", "itac", "il13")
#lf_test = lf_fp_npa[lf_fp_npa$mediator == "il12p70",]
lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,]

foo=doMyPlots(lf_test)
baz=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2)
baz

# entire sample_type data
#bar=doMyPlots(lf_fp_npa)
#bang=cowplot::plot_grid(plotlist=bar, align = 'hv', ncol=7, nrow=5)
#bang

dev.off()