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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(x, ar = 3/5, zrange, map = FALSE, anno)

Arguments

`x`	a `cellHTS` object that has already been scored (i.e. containing the slot `score`).
`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 `x$score`.
`map`	a logical value that determines whether an image map should be created using tooltips to indicate the annotation at each position. It only makes sense to set it to `TRUE` when the function is called from `writeReport`, so the default is `FALSE`.
`anno`	optional input giving the annotation information for the mapping. It should be a vector of the same size as `x$score`. See details.

Details

This function creates an image plot that gives an overview of the whole set of score values from the cellHTS object x, x$score. When the annotation mapping is performed, by default, anno is set to:

The content of x$geneAnno$GeneSymbol (or x$geneAnno$GeneID, if the former is not available), if x is annotated;
The position within the plate, if x is not annotated yet.

Author(s)

Ligia Braz ligia@ebi.ac.uk

Examples

    data(KcViabSmall) 
    x <- KcViabSmall   
    x <- normalizePlates(x, normalizationMethod="median", zscore="-")
    x <- summarizeReplicates(x) 
    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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> library(cellHTS)
Loading required package: grid
Warning message:
Package 'cellHTS' is deprecated and will be removed from Bioconductor
  version 3.4. Please consider using 'cellHTS2' which offers better
  functionality for working with multiple screens and with
  multi-channel screens. 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cellHTS/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, normalizationMethod="median", zscore="-")
>     x <- summarizeReplicates(x) 
>     imageScreen(x, zrange=c(-5,5))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>