#!/usr/bin/Rscript   
getwd()
setwd("~/git/mosaic_2020/")
getwd()
############################################################
# TASK: boxplots at T1
# FIXME: currently not rendering, problem with NAs for stats?
############################################################

#=============
# Input
#=============
source("data_extraction_mediators.R")

# check: adult variable and age variable discrepancy!
metadata_all$mosaic[metadata_all$adult==1 & metadata_all$age<=18]

#===============================
# data assignment for plots
#================================
#-----------
# npa
#-----------
wf_fp_npa = npa_wf[npa_wf$flustat == 1,]
lf_fp_npa = npa_lf[npa_lf$flustat == 1,]
lf_fp_npa$timepoint = paste0("t", lf_fp_npa$timepoint)
lf_fp_npa$timepoint = as.factor(lf_fp_npa$timepoint)
lf_fp_npa$obesity = as.factor(lf_fp_npa$obesity)

table(lf_fp_npa$mediator)
head(lf_fp_npa$value[lf_fp_npa$mediator == "vitd"])
lf_fp_npa = lf_fp_npa[!lf_fp_npa$mediator == "vitd",]
table(lf_fp_npa$mediator)

#-----------
# sam
#-----------
wf_fp_sam = sam_wf[sam_wf$flustat == 1,]
lf_fp_sam = sam_lf[sam_lf$flustat == 1,]
lf_fp_sam$timepoint = paste0("t", lf_fp_sam$timepoint)
lf_fp_sam$timepoint = as.factor(lf_fp_sam$timepoint)
lf_fp_sam$obesity = as.factor(lf_fp_sam$obesity)

table(lf_fp_sam$mediator)
head(lf_fp_sam$value[lf_fp_sam$mediator == "vitd"])
lf_fp_sam = lf_fp_sam[!lf_fp_sam$mediator == "vitd",]
table(lf_fp_sam$mediator)

#-----------
# serum
#-----------
wf_fp_serum = serum_wf[serum_wf$flustat == 1,]
lf_fp_serum = serum_lf[serum_lf$flustat == 1,]
lf_fp_serum$timepoint = paste0("t", lf_fp_serum$timepoint)
lf_fp_serum$timepoint = as.factor(lf_fp_serum$timepoint)
lf_fp_serum$obesity = as.factor(lf_fp_serum$obesity)

head(lf_fp_sam$value[lf_fp_serum$mediator == "vitd"])
########################################################################