tcplPlotFits: Plot summary fits based on fit and dose-response data

In USEPA/CompTox-ToxCast-tcpl: ToxCast Data Analysis Pipeline

Plot summary fits based on fit and dose-response data

Description

tcplPlotFits takes the dose-response and fit data and produces summary plot figures.

Usage

tcplPlotFits(
  dat,
  agg,
  flg = NULL,
  boot = NULL,
  ordr.fitc = FALSE,
  browse = FALSE,
  cnst = NULL,
  orig.aeid = NULL,
  compare = F
)

Arguments

dat	data.table, level 4 or level 5 data, see details.
agg	data.table, concentration-response aggregate data, see details.
flg	data.table, level 6 data, see details.
boot	data.table, level 7 data, see details.
ordr.fitc	Logical, should the fits be ordered by fit category?
browse	Logical, should browser() be called after every plot?
cnst	Constant hline to draw on plot
orig.aeid	Original aeid list from tcplMakeAeidPlts to maintain order
compare	boolean to determine if aeids should be compared on same plot

Details

The data for 'dat', 'agg', and 'flg' should be loaded using the tcplLoadData function with the appropriate 'lvl' parameter. See help page for tcplLoadData for more information.

Supplying level 4 data for the 'dat' parameter will result in level 4 plots. Similarly, supp

If fits are not ordered by fit category, they will be ordered by chemical ID. Inputs with multiple assay endpoints will first be ordered by assay endpoint ID.

Examples

## Store the current config settings, so they can be reloaded at the end 
## of the examples
conf_store <- tcplConfList()
tcplConfDefault()

## tcplPlotFits needs data.tables supplying the concentration/response
## data stored in mc4_agg, as well as the fit information from mc4 or mc5.
## Additionally, tcplPlotFits can take level 6 data from mc6 and add the
## flag information to the plots. The following shows how to make level 5
## plots. Adding the 'flg' parameter would result in level 6 plots, and 
## loading level 4, rather than level 5 data, would result in level 4 plots.
 
l5 <- tcplLoadData(lvl = 5, fld = "m4id", val = 18609966)
l4_agg <- tcplLoadData(lvl = "agg", fld = "m4id", val = 18609966)

## Not run: 
pdf(file = "tcplPlotFits.pdf", height = 6, width = 10, pointsize = 10)
tcplPlotFits(dat = l5, agg = l4_agg)
graphics.off()

## End(Not run)

## While it is most likely the user will want to just save all of the plots 
## to view in a PDF, the 'browse' parameter can be used to quickly view 
## some plots. 

## Start by identifying some sample IDs to plot, then call tcplPlotFits with
## a subset of the data. This browse function is admittedly clunky. 
bpa <- tcplLoadChem(field = "chnm", val = "Bisphenol A")[ , spid]
l5_sub <- l5[spid %in% bpa] 
## Not run: 
tcplPlotFits(dat = l5_sub, 
             agg = l4_agg[m4id %in% l5_sub$m4id], 
             browse = TRUE)

## End(Not run)

## Reset configuration
options(conf_store)
 

USEPA/CompTox-ToxCast-tcpl documentation built on April 22, 2024, 12:37 p.m.