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

In philipmorrisintl/GladiaTOX: R Package for Processing High Content Screening data

Plot summary fits based on fit and dose-response data

Description

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

Usage

gtoxPlotFits(dat, agg, flg = NULL, ordr.fitc = FALSE, bline = "bmad")

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.
ordr.fitc	Logical, should the fits be ordered by fit category?
bline	Character of length 1, the value used for drawing the baseline noise

Details

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

Any values for 'bline' other than 'coff' will use 3*bmad.

Value

None

Examples

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

## gtoxPlotFits needs data.tables supplying the concentration/response
## data stored in mc4_agg, as well as the fit information from mc4 or mc5.
## Additionally, gtoxPlotFits will take level 6 data from mc6 and add the
## flag information to the plots. The following shows how to make level 6
## plots. Omitting the 'flg' parameter would result in level 5 plots, and
## loading level 4, rather than level 5 data, would result in level 4 plots.

aeid = 2
l5 <- gtoxLoadData(lvl = 5, fld = "aeid", val = aeid)
l4_agg <- gtoxLoadData(lvl = "agg", fld = "aeid", val = aeid)
l6 <- gtoxLoadData(lvl = 6, fld = "aeid", val = aeid)
## Not run: 
pdf(file = "gtoxPlotFits.pdf", height = 6, width = 10, pointsize = 10)
gtoxPlotFits(dat = l5, agg = l4_agg, flg = l6)
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 gtoxPlotFits with
## a subset of the data. This browse function is admittedly clunky.
bpa <- gtoxLoadChem(field = "chnm", val = "chromium")[ , spid]
l5_sub <- l5[spid %in% bpa]

gtoxPlotFits(dat = l5_sub, agg = l4_agg[m4id %in% l5_sub$m4id])


## Reset configuration
options(conf_store)

philipmorrisintl/GladiaTOX documentation built on Aug. 27, 2023, 9:07 p.m.