#!/usr/bin/Rscript   
getwd()
setwd("~/git/mosaic_2020/")
getwd()
###############################################################
#=============
# Input
#=============
source("boxplot_stat_function.R")
source("plot_data.R")

#=============
# Output
#=============
outfile_bp = paste0("boxplots_stats_all", ".pdf")
output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
pdf(output_boxplot_stats, width=22, height=16)
###############################################################
#===============================
# data assignment for plots
#===============================
#-------------
# NPA
#-------------
my_sample_npa = "NPA"
fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa

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

plots_npa = doMyPlots(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(my_sample_npa
                                  , color = "blue"
                                  , face = "bold"
                                  , size = 14)
                , bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_npa, ")")
                                   , color = "blue"
                                   , hjust = 1
                                   , x = 0.98
                                   , face = "italic"
                                   , size = 10)
                , left = text_grob("Levels (pg/ml)"
                                   , color = "black"
                                   , rot = 90
                                   , size = 18))
npa_plot_annot
#dev.off()
#-------------
# SAM
#-------------
#my_sample_sam = "SAM"
#fp_sam = length(unique(lf_fp_sam$mosaic)); fp_sam

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

#plots_sam = doMyPlots(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(my_sample_sam
#                                                   , color = "blue"
#                                                   , face = "bold"
#                                                   , size = 14)
#                                 , bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_sam, ")")
#                                                      , color = "blue"
#                                                      , hjust = 1
#                                                      , x = 0.98
#                                                      , face = "italic"
#                                                      , size = 10)
#                                 , left = text_grob("Levels (pg/ml)"
#                                                    , color = "black"
#                                                    , rot = 90
#                                                    , size = 18))
#sam_plot_annot
#dev.off()
#-------------
# SERUM 
#-------------
my_sample_serum = "serum"
fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum

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

plots_serum = doMyPlots(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(my_sample_serum
                                                     , color = "blue"
                                                     , face = "bold"
                                                     , size = 14)
                                   , bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_serum, ")")
                                                        , color = "blue"
                                                        , hjust = 1
                                                        , x = 0.98
                                                        , face = "italic"
                                                        , size = 10)
                                   , left = text_grob("Levels (pg/ml)"
                                                      , color = "black"
                                                      , rot = 90
                                                      , size = 18))
serum_plot_annot
dev.off()
###############################################################