plateView: PLATE VIEW OF RTCA DATA

In RTCA: Open-source toolkit to analyse data from xCELLigence System (RTCA)

Description

Plots a E-plate in RTCA assays in one plot to convey an overview of the plate

Usage

plateView(rtca, ylim, titles,...)

Arguments

rtca	An object of RTCA
ylim	ylab lim
titles	Titles of sub-figures representing each well. If missing, the function seeks whether a Well column is available in the pData of the RTCA object, and if so, its value will be used. If not, the sample names (by sampleNames function) will be used as titles.
...	Other parameters passed to the plot function. Currently options col, lty and lwd are supported. See details below.

Details

For now the function only supports the visualization of a 96-well E-plate.

The plate view plot draws lines indicating cell index (or its transformations) in a birdview. When ... are not specified, default color, line style and width are used. col,lty and lwd can be a vector, and if needed they will be expanded to have the same length as wells.

Value

NULL, the function is called for the side effect

Author(s)

Jitao David Zhang [e-mail]

See Also

RTCA for data structure, plot for the basic plot function.

Examples

require(RTCA)
  
ofile <- system.file("extdata/testOutput.csv", package="RTCA")
rtca <- parseRTCA(ofile)

## Not run automatically, because of 'margin too large'
## plateView(rtca)
## plateView(rtca, lty=2)
## plateView(rtca, col=rep(1:8, each=12))

rtca.skip <- parseRTCA(ofile, maskWell="H[0-9]{2}")
## plateView(rtca.skip)

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: RColorBrewer
Loading required package: gtools
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RTCA documentation built on Nov. 8, 2020, 7:52 p.m.