imageScreen {cellHTS2} | 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:

1. (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`;

2. 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.

### See Also

`normalizePlates`, `summarizeChannels`, `scoreReplicates`, `summarizeReplicates`, `Data` `writeReport`

### 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))

[Package cellHTS2 version 2.46.1 Index]