#!/usr/bin/Rscript   
getwd()
setwd("~/git/mosaic_2020/")
getwd()
###############################################################
# TASK: boxplots with stats for NPA, SAM and SERUM 
# 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_ob_paper.R")

#=============
# Output
#=============
outdir_plots_paper = "/home/tanu/git/mosaic_2020/output/plots_paper/"

#outfile_bp = paste0("boxplots_stats_paper-%03d.png")
#output_boxplot_stats = paste0(outdir_plots_paper, outfile_bp); output_boxplot_stats
#svg(output_boxplot_stats, width=22, height=16)
#png(output_boxplot_stats, width = 11, height = 8, units = "in", res = 300)

###############################################################
#===============================
# data assignment for plots
#===============================
#-------------
# NPA: VL
#-------------
#linear
cat("plotting for FP adult patients:",
      length(unique(vl_lf_plot_df$mosaic)))

# linear : but data is not visible
plots_npa_vl = doMyPlotsStats(vl_lf_plot_df)
npa_plot_vl = ggpubr::ggarrange(plotlist = plots_npa_vl
                             , align = "hv"
                             #, legend = c(0.8,1)
                             #, legend = "bottom"
                             , common.legend = T)
npa_plot_vl

# log
plots_npa_vl_log = doMyPlotsStats(vl_lf_plot_df_log)
npa_plot_vl_log = ggpubr::ggarrange(plotlist = plots_npa_vl_log
                                , align = "hv"
                                , common.legend = T
                                )
npa_plot_vl_log

############################################################
mediator_order = c("IFN-α2a","IFN-β", "IFN-γ", "IL-1", "IL-6", "CXCL8", "CXCL10", "TNF-α")

#-----------------------------
# NPA: selected mediators
#-----------------------------
# linear
plots_npa = doMyPlotsStats(npa_lf_plot_df, custom_order = mediator_order)
npa_plot_1 = ggpubr::ggarrange(plotlist = plots_npa
                             , align = "hv"
                             , ncol = 8
                             , nrow = 1
                             , common.legend = T)
npa_plot = annotate_figure(npa_plot_1,
                           top = text_grob("NPA"
                                           , color = "black"
                                           #, face = "bold"
                                           , size = 14))

# log
plots_npa_log = doMyPlotsStats(npa_lf_plot_df_log, custom_order = mediator_order)
npa_plot_log_1 = ggpubr::ggarrange(plotlist = plots_npa_log
                             , align = "hv"
                             , ncol = 8
                             , nrow = 1
                             , common.legend = T)
npa_plot_log = annotate_figure(npa_plot_log_1,
                               top = text_grob("NPA"
                                               , color = "black"
                                               #, face = "bold"
                                               , size = 14))
npa_plot_log
#-------------------------------
# SERUM: selected mediators
#--------------------------------
# linear
plots_serum = doMyPlotsStats(serum_lf_plot_df, custom_order = mediator_order)
serum_plot_1 = ggpubr::ggarrange(plotlist = plots_serum
                               , align = "hv"
                               , ncol = 8
                               , nrow = 1
                               , common.legend = F
                               )

serum_plot =  annotate_figure(serum_plot_1,
                               top = text_grob("Serum"
                                               , color = "black"
                                               #, face = "bold"
                                               , size = 14))
serum_plot

# log
plots_serum_log = doMyPlotsStats(serum_lf_plot_log, custom_order = mediator_order)
serum_plot_log_1 = ggpubr::ggarrange(plotlist = plots_serum_log
                                 , align = "hv"
                                 , ncol = 8
                                 , nrow = 1
                                 , common.legend = F)

serum_plot_log = annotate_figure(serum_plot_log_1,
                                 top = text_grob("Serum"
                                                 , color = "black"
                                                 #, face = "bold"
                                                 , size = 14))

serum_plot_log

##############################################################
##############################################################
cat ("Outplots will be in:", outdir_plots_paper)
#======================
# Output: Linear graphs
#======================
# viral load: linear
viral_load_annot = annotate_figure(
  npa_plot_vl
  , left = text_grob("pg/ml"
                     , color = "black"
                     , rot = 90
                     , size = 18)
)

png(paste0(outdir_plots_paper, "viral_load_linear"),
    width = 5,
    height = 5,
    units = "in",
    res = 300)

viral_load_annot
dev.off()

# npa and serum mediators: linear
outplot_linear = cowplot::plot_grid(
  npa_plot,
  serum_plot,
  nrow = 2,
  rel_heights = c(1.15,1)
)

outplot_linear_annot = annotate_figure(
  outplot_linear
  , left = text_grob("pg/ml"
                     , color = "black"
                     , rot = 90
                     , size = 16)
)

png(paste0(outdir_plots_paper, "npa_serum_linear"),
    width = 18,
    height = 6,
    units = "in", 
    res = 300)
outplot_linear_annot
dev.off()


#======================
# Output: Log graphs
#======================
# viral load: log
viral_load_log_annot = annotate_figure(
  npa_plot_vl_log
  , left = text_grob("Log10 (pg/ml)"
                     , color = "black"
                     , rot = 90
                     , size = 18)
)

png(paste0(outdir_plots_paper, "viral_load_log" ),
    width = 5,
    height = 5,
    units = "in",
    res = 300)

viral_load_log_annot
dev.off()

# npa and serum mediators: log
outplot_log = cowplot::plot_grid(
  npa_plot_log,
  serum_plot_log,
  nrow = 2,
  rel_heights = c(1.15,1)
  )


outplot_log_annot = annotate_figure(
  outplot_log
  , left = text_grob("Log10 (pg/ml)"
                     , color = "black"
                     , rot = 90
                     , size = 16)
)
  
png(paste0(outdir_plots_paper, "npa_serum_log"),
    width = 18,
    height = 6,
    units = "in", 
    res = 300)
outplot_log_annot
dev.off()


###############################################################
#                         END OF SCRIPT                       #
###############################################################