gtoxPlotPlate: Plot plate heatmap

In pmpsa-hpc/GladiaTOX: R Package for Processing High Content Screening data

Plot plate heatmap

Description

gtoxPlotPlate generates a heatmap of assay plate data

Usage

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

Arguments

dat	data.table containing gtox 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 indcate 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.

Value

None

Note

For the optimal output size, use width = 12, height = 8, pointsize = 12, units = "in"

Examples

## Define assay component and extract assay component ID
acnm <- "Cytotoxicity (TIER1)_Cytochrome C release_24h"
acid <- gtoxLoadAcid(fld=c("asid", "acnm"), val=list(1L,acnm))[, acid]
## Extract assay plate ID corresponding to plate name S-000049119
apid <- gtoxLoadApid()[u_boxtrack == "S-000049119", apid]
## Load level 2 data (Raw data before normalization)
l2 <- gtoxLoadData(lvl = 2L, fld = "acid", val = acid)
gtoxPlotPlate(dat = l2, apid = apid, id = acid)

pmpsa-hpc/GladiaTOX documentation built on Sept. 1, 2023, 5:52 p.m.