imageScreen {cellHTS} | 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:

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

### Author(s)

Ligia Braz ligia@ebi.ac.uk

### See Also

`normalizePlates`, `summarizeChannels`, `summarizeReplicates`, `writeReport`

### Examples

        data(KcViabSmall)
        x <- KcViabSmall
        x <- normalizePlates(x, normalizationMethod="median", zscore="-")
        x <- summarizeReplicates(x)
        imageScreen(x, zrange=c(-5,5))

[Package cellHTS version 1.10.0 Index]