#!/usr/bin/Rscript   
getwd()
setwd("~/git/mosaic_2020/")
getwd()
###############################################################
# TASK: boxplots with stats for NPA, SAM and SERUM but with log scale
# for each mediator, at each timepoint, by group

# TODO: check boxplot_stat_function.R
# output plots even if stats fail due to data containing only LLODs
# however for a given mediator, if there is error for ANY timepoint
# stats will not be added for the entire plot! To be handled in 
# next iteration!
###############################################################

#=============
# Input
#=============
source("boxplot_stat_function.R")
source("plot_data_s.R")

#=============
# Output
#=============
outfile_bp = paste0("boxplots_stats_all_Sev_LOG-%03d.svg")
output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
svg(output_boxplot_stats, width=22, height=16)
###############################################################
#===============================
# data assignment for plots
#===============================
#----------------------------------------
#-------
# NPA
#-------
# vl data juggling with 0!
vl_temp_fix = lf_fp_npa[lf_fp_npa$mediator=="vl_pfu_ul",]
vl_temp_fix$value[1:20]
vl_temp_fix$value[vl_temp_fix$value == 0] <- 1
vl_temp_fix$value[1:20]

orig_nrow = nrow(lf_fp_npa); orig_nrow; table(lf_fp_npa$mediator)
lf_fp_npa = lf_fp_npa[!lf_fp_npa$mediator=="vl_pfu_ul",]
temp_nrow = nrow(lf_fp_npa); temp_nrow; table(lf_fp_npa$mediator)

# add vl_temp_fix back
lf_fp_npa = rbind(lf_fp_npa, vl_temp_fix)
revised_nrow = nrow(lf_fp_npa); revised_nrow

orig_nrow == revised_nrow

head(lf_fp_npa$value)
#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
# log all values and reassign
#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
lf_fp_npa$value = log10(lf_fp_npa$value)
head(lf_fp_npa$value)
vl_temp_fix2 = lf_fp_npa[lf_fp_npa$mediator=="vl_pfu_ul",]
vl_temp_fix2$value[1:20]

#------------------------------------------
title_npa = "NPA (severe)"
fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa

cat("\nPlotting boxplots with stats for:", title_npa
    , "\n========================================================\n")

plots_npa = doMyPlotsStats(lf_fp_npa)
npa_plot = ggpubr::ggarrange(plotlist = plots_npa
                             , align = "hv"
                             , ncol = 7
                             , nrow = 5
                             , common.legend = T)
#npa_plot
npa_plot_annot = annotate_figure(npa_plot
                , top = text_grob(title_npa
                                  , color = "blue"
                                  , face = "bold"
                                  , size = 18)
                , bottom = text_grob(paste0("Mosaic data\nFP severe adults (n=", fp_npa, ")")
                                   , color = "blue"
                                   , hjust = 1
                                   , x = 0.98
                                   , face = "italic"
                                   , size = 15)
                , left = text_grob("Levels (pg/ml)"
                                   , color = "black"
                                   , rot = 90
                                   , size = 18))
npa_plot_annot
#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#
#-------------
# SAM
#-------------
head(lf_fp_sam$value)

#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
# log all values and reassign
#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
lf_fp_sam$value = log10(lf_fp_sam$value)
head(lf_fp_sam$value)

title_sam = "SAM (severe)"
fp_sam = length(unique(lf_fp_sam$mosaic)); fp_sam

cat("\nPlotting boxplots with stats for:", title_sam
    , "\n========================================================\n")

plots_sam = doMyPlotsStats(lf_fp_sam)
sam_plot = ggpubr::ggarrange(plotlist = plots_sam
                             , align = "hv"
                             , ncol = 7
                             , nrow = 5
                             , common.legend = T)
#sam_plot
sam_plot_annot = annotate_figure(sam_plot
                                 , top = text_grob(title_sam
                                                   , color = "blue"
                                                   , face = "bold"
                                                   , size = 18)
                                 , bottom = text_grob(paste0("Mosaic data\nFP severe adults (n=", fp_sam, ")")
                                                      , color = "blue"
                                                      , hjust = 1
                                                      , x = 0.98
                                                      , face = "italic"
                                                      , size = 15)
                                 , left = text_grob("Levels (pg/ml)"
                                                    , color = "black"
                                                    , rot = 90
                                                    , size = 18))
sam_plot_annot
#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#
#------------------------------------------
#-------------
# SERUM 
#-------------
head(lf_fp_serum$value)
#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
# log all values and reassign
#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
lf_fp_serum$value = log10(lf_fp_serum$value)
head(lf_fp_serum$value)

title_serum = "SERUM (severe)"
fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum

cat("\nPlotting boxplots with stats for:", title_serum
    , "\n========================================================\n")

plots_serum = doMyPlotsStats(lf_fp_serum)
serum_plot = ggpubr::ggarrange(plotlist = plots_serum
                               , align = "hv"
                               , ncol = 7
                               , nrow = 5
                               , common.legend = T)
#serum_plot
serum_plot_annot = annotate_figure(serum_plot
                                   , top = text_grob(title_serum
                                                     , color = "blue"
                                                     , face = "bold"
                                                     , size = 18)
                                   , bottom = text_grob(paste0("Mosaic data\nFP severe adults (n=", fp_serum, ")")
                                                        , color = "blue"
                                                        , hjust = 1
                                                        , x = 0.98
                                                        , face = "italic"
                                                        , size = 15)
                                   , left = text_grob("Levels (pg/ml)"
                                                      , color = "black"
                                                      , rot = 90
                                                      , size = 18))
serum_plot_annot
dev.off()
###############################################################
#                         END OF SCRIPT                       #
###############################################################