Screen plot of the plate configuration of a cellHTS object

Description

Screen plot displaying the plate configuration of a cellHTS object.

Usage

configurationAsScreenPlot(x, verbose=interactive(), posControls,
negControls, legend=FALSE, main="")

Arguments

Details

This function calls the function plotScreen to create a screen plot showing the plate configuration (as defined by the plate configuration file used to configure the cellHTS object – see function configure) used for the RNAi experiment stored in x.

posControls and negControls should be given as vectors of regular expression patterns specifying the name(s) of the positive(s) and negative(s) controls, respectivey, as provided in the plate configuration file (and acccessed via wellAnno(x)).

By default, if posControls is not given, "pos" will be taken as the annotation name for the wells containing positive controls. Similarly, if negControls is missing, by default "neg" will be considered as the name used to annotate the negative controls. The content of posControls and negControls will be passed to regexpr for pattern matching within the well annotation given in column controlStatus of the featureData slot of the cellHTS object.

Value

Invisibly, a vector with the color map used to display the well annotation in the image plot.

Author(s)

Ligia Bras ligia@ebi.ac.uk

References

Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.

See Also

plotScreen, writeReport

Examples

    data("KcViab") 
    configurationAsScreenPlot(KcViab)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(cellHTS2)
Loading required package: RColorBrewer
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

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

Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cellHTS2/configurationAsScreenPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: configurationAsScreenPlot
> ### Title: Screen plot of the plate configuration of a cellHTS object
> ### Aliases: configurationAsScreenPlot
> 
> ### ** Examples
> 
>     data("KcViab") 
>     configurationAsScreenPlot(KcViab)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>