#!/usr/bin/Rscript   
getwd()
setwd("~/git/mosaic_2020/")
getwd()
###############################################################
source("boxplot_stat_function.R")
source("plot_data.R")
#============= 
# Output TEST
#=============
my_sample_name = "SAM"
to_remove = c("ifna2a", "il29")
lf_fp_sam2 = lf_fp_sam[!lf_fp_sam$mediator%in%to_remove,]
lf_fp_sam3 = lf_fp_sam[lf_fp_sam$mediator%in%to_remove,]

foo = doMyPlots(lf_fp_sam2)

outfile_bp = paste0("boxplots_TEST_", my_sample_name, ".pdf")
output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
pdf(output_boxplot_stats, width=22, height=16)

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

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

sam_plot = ggpubr::ggarrange(plotlist = foo
                             , align = "hv"
                             , ncol = 7
                             , nrow = 5
                             , common.legend = T)
sam_plot
foo_annot = annotate_figure(sam_plot
                            , top = text_grob(my_sample_name
                                              , 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)
)
foo_annot
dev.off()
##################################################################
# ind components of function
my_sample_name = "SAM"
to_remove = c("ifna2a"
              , "il29")

lf_fp_sam2 = lf_fp_sam[!lf_fp_sam$mediator%in%to_remove,]
lf_fp_sam3 = lf_fp_sam[lf_fp_sam$mediator%in%to_remove,]

df_test = lf_fp_sam3
df_test = lf_fp_sam2
table(df_test$mediator)

p = ggplot(df_test)+ geom_boxplot(aes(x = timepoint
                                     , y = value
                                     , color = obesity
                                     #, palette = c("#00BFC4", "#F8766D")
))+
  scale_colour_manual(values=c("#00BFC4", "#F8766D")) + 
  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_blank()
        , legend.position = "none"
        , plot.subtitle = element_text(size = 20, hjust = 0.5)
        , plot.title = element_text(size = 20, hjust = 0.5)) +
  labs(title = "TEST")
p

#--------
# stats
#---------
to_remove = c("ifna2a"
              , "il29")
lf_fp_sam3 = lf_fp_sam[lf_fp_sam$mediator%in%to_remove,]

lf_fp_sam4 = lf_fp_sam3[lf_fp_sam3$timepoint == "t3",]
table(lf_fp_sam4$timepoint)

wilcox_test(value~obesity, data = lf_fp_sam4)

table(lf_fp_sam3$mediator, lf_fp_sam3$timepoint)
time = c("t3")
lf_fp_sam3 = lf_fp_sam3[!lf_fp_sam3$timepoint%in%time,]
table(lf_fp_sam3$mediator, lf_fp_sam3$timepoint)

med = c("il29")
time2 = c("t2")

lf_fp_sam3 = lf_fp_sam3[!lf_fp_sam3$mediator%in%med && lf_fp_sam3$timepoint%in%time2,]
table(lf_fp_sam3$mediator, lf_fp_sam3$timepoint)

df_test = lf_fp_sam3


table(df_test$mediator)


stat_df <- df_test %>%
  group_by(timepoint, mediator) %>%
  wilcox_test(value ~ obesity, paired = F) %>%
  add_significance("p")
stat_df$p_format = round(stat_df$p, digits = 3)


stat_df <- stat_df %>%
  add_xy_position(x = "timepoint", dodge = 0.8)
p2 = p + stat_pvalue_manual(stat_df
                            #, y.position = max_y
                            , label = "{p_format} {p.signif}"
                            , hide.ns = T
                            , tip.length = 0)+
  scale_y_continuous(expand = expansion(mult = c(0.05, 0.25)))

p2