---
title: "Ring et al. 2017 Plotting Css95"
author: "Caroline Ring"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Plotting Css95}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include=FALSE}
knitr::opts_chunk$set(collapse = TRUE, comment = '#>')
```

This vignette contains the code to plot Css95 values vs. independent MC (Supplemental Figures).

```{r, eval = FALSE}
library('data.table')
library('ggplot2')
library('httk')
library('reshape2')
```
First, we set up a function to read in the data files and do some reshaping.

```{r, eval=FALSE}
data_read <- function(model, poormetab, fup.censor, chemlist){
httk.dat <- readRDS(paste0('data/',
                      paste('allchems', 'indepMC',
                            'poormetab', poormetab,
                            'fup.censor', fup.censor,
                            model, "FuptoFub", sep='_'),
                      '.Rdata'))

httk.LCL <- melt(httk.dat[, 
                                       c('chemcas', 
                                         grep(x=names(httk.dat), 
                                              pattern='LCLcss', 
                                              value=TRUE)), 
                                       with=FALSE], 
                         measure.vars=grep(x=names(httk.dat), 
                                           pattern='LCLcss', 
                                           value=TRUE),
                         variable.name='pctile',
                         value.name='LCL')
httk.LCL[, pctile:=as.numeric(gsub(x=pctile,
                                           pattern='LCLcss',
                                           replacement=''))]
httk.UCL <- melt(httk.dat[, 
                          c('chemcas', 
                            grep(x=names(httk.dat), 
                                 pattern='UCLcss', 
                                 value=TRUE)), 
                          with=FALSE], 
                 measure.vars=grep(x=names(httk.dat), 
                                   pattern='UCLcss', 
                                   value=TRUE),
                 variable.name='pctile',
                 value.name='UCL')
httk.UCL[, pctile:=as.numeric(gsub(x=pctile,
                                   pattern='UCLcss',
                                   replacement=''))]

httk.cssval <- melt(httk.dat[, 
                                       c('chemcas', 
                                         grep(x=names(httk.dat), 
                                              pattern='(?<!CL)css\\d{1}', 
                                              perl=TRUE, 
                                              value=TRUE)), 
                                       with=FALSE], 
                         measure.vars=grep(x=names(httk.dat), 
                                           pattern='(?<!CL)css\\d{1}', 
                                           perl=TRUE, 
                                           value=TRUE),
                         variable.name='pctile',
                         value.name='css')
httk.cssval[, pctile:=as.numeric(gsub(x=pctile,
                                           pattern='css',
                                           replacement=''))]
httk.tmp <- merge(httk.cssval, 
                       httk.LCL, 
                       by=c('chemcas',
                            'pctile'))
httk.tmp <- merge(httk.tmp,
                  httk.UCL,
                  by=c('chemcas',
                       'pctile'))
httk.tmp[, method:='independentMC']
httk.tmp[, ExpoCast.group:='none']

ExpoCast.groups<-list("Total",
                      "Age.6.11",
                      "Age.12.19",
                      "Age.20.65",
                      "Age.GT65",
                      "BMIgt30",
                      "BMIle30",
                      "Females",
                      "Males",
                      "ReproAgeFemale",
                      "Age.20.50.nonobese")

tmpfun <- function(grp, popmethod, poormetab, fup.censor){
  tmp.dt <- readRDS(paste0('data/',
                              paste('allchems', grp, popmethod,
                                    'poormetab', poormetab,
                                    'fup.censor', fup.censor,
                                    model, "FuptoFub", sep='_'),
                              '.Rdata'))
  tmp.dt[, ExpoCast.group:=grp]
  return(tmp.dt)
  
}
httkpop.dat <- rbindlist(lapply(ExpoCast.groups, tmpfun, popmethod='dr',
                                poormetab=poormetab,
                                fup.censor=fup.censor))

httkpop.LCL <- melt(httkpop.dat[, 
                                    c('chemcas', 
                                      grep(x=names(httkpop.dat), 
                                           pattern='LCLcss', 
                                           value=TRUE),
                                      'ExpoCast.group'), 
                                    with=FALSE], 
                      measure.vars=grep(x=names(httkpop.dat), 
                                        pattern='LCLcss', 
                                        value=TRUE),
                      variable.name='pctile',
                      value.name='LCL')
httkpop.LCL[, pctile:=as.numeric(gsub(x=pctile,
                                        pattern='LCLcss',
                                        replacement=''))]

httkpop.UCL <- melt(httkpop.dat[, 
                               c('chemcas', 
                                 grep(x=names(httkpop.dat), 
                                      pattern='UCLcss', 
                                      value=TRUE),
                                 'ExpoCast.group'), 
                               with=FALSE], 
                      measure.vars=grep(x=names(httkpop.dat), 
                                        pattern='UCLcss', 
                                        value=TRUE),
                      variable.name='pctile',
                      value.name='UCL')
httkpop.UCL[, pctile:=as.numeric(gsub(x=pctile,
                                        pattern='UCLcss',
                                        replacement=''))]

httkpop.cssval <- melt(httkpop.dat[, 
                                       c('chemcas', 
                                         grep(x=names(httkpop.dat), 
                                              pattern='(?<!CL)css\\d{1}', 
                                              perl=TRUE, 
                                              value=TRUE), 
                                         'ExpoCast.group'), 
                                       with=FALSE], 
                         measure.vars=grep(x=names(httkpop.dat), 
                                           pattern='(?<!CL)css\\d{1}', 
                                           perl=TRUE, 
                                           value=TRUE),
                         variable.name='pctile',
                         value.name='css')
httkpop.cssval[, pctile:=as.numeric(gsub(x=pctile,
                                           pattern='css',
                                           replacement=''))]
httkpop.tmp <- merge(httkpop.cssval, 
                       httkpop.LCL, 
                       by=c('chemcas',
                            'ExpoCast.group',
                            'pctile'))
httkpop.tmp <- merge(httkpop.tmp,
                       httkpop.UCL,
                       by=c('chemcas',
                            'ExpoCast.group',
                            'pctile'))
httkpop.tmp[, method:='dr']

m.dat <- rbindlist(list(httkpop.tmp,  
               httk.tmp), 
               use.names=TRUE)
m.dat <- merge(m.dat, chemlist, by='chemcas') #Add compound name and MW columns
m.dat[, poormetab:=poormetab]
m.dat[, fup.censor:=fup.censor]

paramfun <- switch(model,
                   '3compartmentss'='parameterize_steadystate',
                   '3compartment'='parameterize_3comp',
                   'pbtk'='parameterize_pbtk',
                   '1compartment'='parameterize_1comp')
paramfunargs <- '(chem.cas=chemcas, species="Human", default.to.human=TRUE)'
if (model!='1compartment'){
p.dt <- chemlist[, eval(parse(text=paste(paramfun,
                                           paramfunargs))),
                   by=chemcas]
}


if (model=='1compartment'){ #get metabolism by doing steady-state parameterization
  p.dt <- chemlist[, eval(parse(text=paste('parameterize_steadystate',
                                            paramfunargs))),
                    by=chemcas]
}

metabname <- switch(model, 
                    '3compartmentss'='Clint',
                    '3compartment'='Clmetabolismc',
                    'pbtk'='Clmetabolismc',
                    '1compartment'='Clint')

m.dat<-merge(m.dat,
      p.dt[, c('chemcas',
               metabname,
               'Funbound.plasma'),
           with=FALSE],
      by='chemcas')

setnames(m.dat,
         c(metabname,
                  'Funbound.plasma'),
         c('metab',
           'fup'))


m.dat[, fup.lod:=factor(ifelse(fup<=0.01, TRUE, FALSE),
                        levels=c(TRUE, FALSE),
                        labels=c('below LOD',
                                 'above LOD'))]
m.dat[, metab.zero:=factor(ifelse(metab==0, TRUE, FALSE),
                           levels=c(TRUE, FALSE),
                           labels=c('zero',
                                    'nonzero'))]

return(m.dat)
}
```

Then we read in the data.
```{r, eval=FALSE}
model <- '3compartmentss'
css.method <- 'analytic'
use.seed <- TRUE
pmlist <- c(TRUE, FALSE)
fclist <- c(TRUE, FALSE)
pmfc <- expand.grid(poormetab=pmlist,fup.censor=fclist)
chemlist <- as.data.table(get_cheminfo(info=c('CAS', 'Compound', 'MW'),
                                         species='Human',
                                         model=model,
                                         exclude.fub.zero=FALSE))
  setnames(chemlist, 'CAS', 'chemcas')
  
  data.read.list <- mapply(data_read,
                           fup.censor=pmfc$fup.censor,
                           poormetab=pmfc$poormetab,
                           MoreArgs=list(model='3compartmentss',
                                         chemlist=chemlist),
                           SIMPLIFY=FALSE)
  m.dat <- rbindlist(data.read.list)
```

We then need to cast m.dat so we can compare the Css percentiles directly.

```{r, eval=FALSE}
methodvect <- c('dr', 'independentMC')
pctilevect <- c(5, 50, 95)
#First: cast the data table into appropriate form
tmp.css<-dcast.data.table(m.dat[method %in% methodvect &
                                  pctile %in% pctilevect], 
                          Compound+chemcas+ExpoCast.group+pctile+fup.lod+
                            metab.zero+fup.censor+poormetab+metab+fup~method, 
                          value.var=c('css'))
setnames(tmp.css, methodvect,
        paste(methodvect,
              'css',
              sep='.'))
tmp.LCL <- dcast.data.table(m.dat[method %in% methodvect &
                                    pctile %in% pctilevect], 
                            Compound+chemcas+ExpoCast.group+pctile+
                              fup.lod+metab.zero+fup.censor+poormetab+metab+fup~method, 
                            value.var=c('LCL'))
setnames(tmp.LCL, methodvect,
         paste(methodvect,
               'LCL',
               sep='.'))
tmp.UCL <- dcast.data.table(m.dat[method %in% methodvect &
                                    pctile %in% pctilevect], 
                            Compound+chemcas+ExpoCast.group+pctile+
                              fup.lod+metab.zero+fup.censor+poormetab+metab+fup~method, 
                            value.var=c('UCL'))
setnames(tmp.UCL, methodvect,
         paste(methodvect,
               'UCL',
               sep='.'))
tmp <- merge(tmp.css,
             tmp.LCL,
             by=c('Compound',
                  'chemcas',
                  'ExpoCast.group',
                  'pctile',
                  'fup.lod',
                  'metab.zero',
                  'poormetab',
                  'fup.censor',
                  'metab',
                  'fup'))
tmp <- merge(tmp,
             tmp.UCL,
             by=c('Compound',
                  'chemcas',
                  'ExpoCast.group',
                  'pctile',
                  'fup.lod',
                  'metab.zero',
                  'poormetab',
                  'fup.censor',
                  'metab',
                  'fup'))
```

And we need to handle the independent MC values properly.

```{r, eval=FALSE}
 xonlynames<-c('dr.css',
                                                           'dr.UCL',
                                                           'dr.LCL')
                                              yonlynames<-c('independentMC.css',
                                                           'independentMC.LCL',
                                                           'independentMC.UCL')
#Handle the independent MC numbers properly
tmp.httk <- tmp[ExpoCast.group=='none',]
tmp[, (yonlynames):=NULL, with=FALSE]
tmp.httkpop <- tmp[ExpoCast.group!='none',]
tmp.httk[, (xonlynames):=NULL, with=FALSE]
tmp.httk[, ExpoCast.group:=NULL]
tmp.merge <- merge(tmp.httkpop, 
                   tmp.httk, 
                   by=c('Compound',
                        'chemcas', 
                        'pctile',
                        'fup.lod', 
                        'metab.zero',
                        'poormetab',
                        'fup.censor',
                        'metab',
                        'fup'))
tmp <- copy(tmp.merge)
```

```{r, eval=FALSE}
ExpoCast.groups<-list("Total",
                      "Age.6.11",
                      "Age.12.19",
                      "Age.20.65",
                      "Age.GT65",
                      "BMIgt30",
                      "BMIle30",
                      "Females",
                      "Males",
                      "ReproAgeFemale",
                      "Age.20.50.nonobese")
 tmp[, poormetab:=factor(poormetab,
                          levels=c(TRUE, FALSE),
                          labels=c('included', 'excluded'))]
  setnames(tmp, 'fup.censor', 'Fub') #rename this column for better labeling
  tmp[, Fub:=factor(Fub,
                    levels=c(TRUE, FALSE),
                    labels=c('<lod censored', '<lod=lod/2'))]
  tmp[, metab.zero:=factor(metab.zero, levels=c('nonzero', 'zero'))]
  tmp[, fup.lod:=factor(fup.lod)]
  tmp[, metab.zero.fup.lod:=factor(paste('CLint',
                                         paste0(metab.zero, ','),
                                         'Fub',
                                         fup.lod))]
  tmp[, ExpoCast.group:=factor(ExpoCast.group, 
                           levels=ExpoCast.groups)]
```

Now, do the plotting by subsets of demographic groups.

```{r, eval=FALSE}
 subset.list <- list(age=c('Total', 
                            'Age.6.11', 
                            'Age.12.19',
                            'Age.20.65',
                            'Age.GT65'),
                      bmi=c('Total', 
                            'BMIle30',
                            'BMIgt30'),
                      sex=c('Total', 
                            'Males',
                            'Females',
                            'ReproAgeFemale'))

axis.text.size <- 1.2
axis.title.size <- 1.2
legend.text.size <- 1.2
point.size <- 1.5
legend.title.size <- 1.2
strip.text.size <- 1.2
for (pct in c(5,50,95)){
    for (i in seq_along(subset.list)){
       
       p <- ggplot(data=tmp[pctile==pct & 
                                      ExpoCast.group %in% subset.list[[i]],]) + 
  geom_point(aes(x=independentMC.css,
                 y=dr.css,
                 color=ExpoCast.group),
             alpha=0.3,
             size=point.size) +
  scale_x_log10() +
  scale_y_log10() +
  geom_abline(slope=1,intercept=0)+
  facet_grid(poormetab~Fub, labeller=labeller(poormetab=function(x) paste("CLint: PMs", x), Fub=label_both)) + 
  scale_color_brewer(type='qual', palette=2) +
  labs(x=bquote(paste(C[ss]^.(pct), '(uM) using independent MC')), 
       y=bquote(paste(C[ss]^.(pct), '(uM) using HTTK-Pop')),
       color='Demographic') +
  guides(color=guide_legend(override.aes=list(size=4,alpha=1)))+
  theme_bw() +
  theme(strip.background=element_blank(),
        legend.key=element_blank(),
        legend.title=element_text(size=rel(legend.title.size)),
        axis.text.x=element_text(size=rel(axis.text.size)),
        axis.text.y=element_text(size=rel(axis.text.size)),
        axis.title.x=element_text(size=rel(axis.title.size)),
        axis.title.y=element_text(size=rel(axis.title.size)),
        legend.text=element_text(size=rel(legend.text.size)),
        strip.text=element_text(size=rel(strip.text.size)))
      
  ggsave(plot=p,
         filename=paste0('pdf_figures/',
                                        'cssplot_',
                                        names(subset.list)[i],
                                        '_drvsindep_',
                                        model,
                                        '_',
                                        pct,
                         "FuptoFub",
                                        '.pdf'),
         width=11,
         height=8.5)
  print(p)
    }
  }
```
