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Last data update: 2014.03.03

R: Experiment-wide quality control plot of a cellHTS object

imageScreen

R Documentation

Experiment-wide quality control plot of a cellHTS object

Description

Experiment-wide quality control plot of a scored cellHTS object.

Usage

imageScreen(object, ar=3/5, zrange=NULL, map=FALSE, anno=NULL,
            col=list(posNeg=rev(brewer.pal(11,
                 "RdBu"))[c(1:5, rep(6, 3), 7:11)], pos=brewer.pal(9,
                 "Greys")), nbImageBins=256, nbLegendBins=7)

Arguments

`object`	a `cellHTS` object that has already been scored (i.e. `state(object)['scored']=TRUE`).
`ar`	the desired aspect ration for the image plot (i.e. number of columns per number of rows)
`zrange`	the range of values to be mapped into the color scale. If missing, `zrange` will be set to the range of the score values stored in slot `assayData` of `object`.
`map`	a logical value that determines whether an image map should be created using tooltips to indicate the annotation at each position. It only makes sense to set it to `TRUE` when the function is called from `writeReport` function, so the default is `FALSE`.
`anno`	optional input giving the annotation information for the mapping. It should be a vector of the same size as the total number of featured in `object`. See details.
`col`	a list giving the colors for the plot. The first element `posNeg` is used if `zrange[1]<0` and `zrange[2]>0`, the second if all values are either positive or negative.
`nbImageBins`	The number of color bins used in the map. Default is 256.
`nbLegendBins`	The number of color bins shown in the legend. Default is 7.

Details

This function creates an image plot that gives an overview of the whole set of score values stored in slot assayData of a scored cellHTS object. When the annotation mapping is performed, by default, anno is set to:

(if object is annotated) The content of column named GeneSymbol or named GeneID (if the former is not available) of the featureData slot of object;
The position within the plate, if object is not annotated.

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.

Examples

    data(KcViabSmall) 
    x <- KcViabSmall   
    x <- normalizePlates(x, scale="multiplicative", log=FALSE, method="median", varianceAdjust="none")
    x <- scoreReplicates(x, sign="-", method="zscore") 
    x <- summarizeReplicates(x, summary="min") 
    imageScreen(x, zrange=c(-5,5))

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)

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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/imageScreen.Rd_%03d_medium.png", width=480, height=480)
> ### Name: imageScreen
> ### Title: Experiment-wide quality control plot of a cellHTS object
> ### Aliases: imageScreen
> ### Keywords: manip
> 
> ### ** Examples
> 
>     data(KcViabSmall) 
>     x <- KcViabSmall   
>     x <- normalizePlates(x, scale="multiplicative", log=FALSE, method="median", varianceAdjust="none")
>     x <- scoreReplicates(x, sign="-", method="zscore") 
>     x <- summarizeReplicates(x, summary="min") 
>     imageScreen(x, zrange=c(-5,5))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>