#!/usr/bin/Rscript   
getwd()
setwd("~/git/mosaic_2020/")
getwd()
###############################################################
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)

#===========================
# NPA
#===========================
my_sample_npa = "NPA"
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("Mosaic data\nFlu positive adults (n=133)"
                                   , 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"
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("Mosaic data\nFlu positive adults (n=133)"
                                                      , 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"
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("Mosaic data\nFlu positive adults (n=133)"
                                                        , 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()