tcplPlotPlate: Plot plate heatmap

Description Usage Arguments Details Note Examples

View source: R/tcplPlotPlate.R

Description

tcplPlotPlate generates a heatmap of assay plate data

Usage

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tcplPlotPlate(dat, apid, id = NULL, quant = c(0.001, 0.999))

Arguments

dat

data.table containing tcpl data

apid

Character of length 1, the apid to plot

id

Integer of length 1, the assay component id (acid) or assay endpoint id (aeid), depending on level. Only need to specify for multiplexed assays when more than one acid/aeid share an apid.

quant

Numeric vector, the range of data to include in the legend

Details

The legend represents the range of the data supplied to dat, for the applicable ID. The additional horizontal lines on the legend indicate the range of the plotted plate, to show the relation of the plate to the assay as a whole. A plot with a legend specific for the given apid can be created by only supplying the data for the apid of interest to 'dat'.

The quant parameter, by default including 99.8 allows for extreme outliers without losing resolution. Outliers in either direction will be highlighted with a dark ring, as seen in the example. A NULL value for 'quant' will not restrict the data at all, and will use the full range for the legend.

Wells with a well quality of 0 (only applicable for level 1 plots), will have an "X" through their center.

Note

For the optimal output size, use width = 10, height = 10*(2/3), pointsize = 10, units = "in"

Examples

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## Store the current config settings, so they can be reloaded at the end 
## of the examples
conf_store <- tcplConfList()
tcplConfDefault()
 
d1 <- tcplLoadData(lvl = 1, fld = "acid", val = 1)
## Not run: 
tcplPlotPlate(dat = d1, apid = "09Apr2014.Plate.17")

## End(Not run)

## Reset configuration
options(conf_store)
 

USEPA/CompTox-ToxCast-tcpl documentation built on May 5, 2019, 4:48 p.m.