Description Usage Arguments Details Examples
tcplPlotFits
takes the dose-response and fit data and produces
summary plot figures.
1 | tcplPlotFits(dat, agg, flg = NULL, ordr.fitc = FALSE, browse = FALSE)
|
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? |
browse |
Logical, should |
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 | ## 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 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.
l5 <- tcplLoadData(lvl = 5, fld = "aeid", val = 1)
l4_agg <- tcplLoadData(lvl = "agg", fld = "aeid", val = 1)
l6 <- tcplLoadData(lvl = 6, fld = "aeid", val = 1)
## Not run:
pdf(file = "tcplPlotFits.pdf", height = 6, width = 10, pointsize = 10)
tcplPlotFits(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 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)
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