plotCtArray {HTqPCR} | R Documentation

## Image plot of qPCR Ct values from an array format

### Description

Function for plotting high-throughput qPCR Ct values from a platform with a defined spatial layout, such as Fluidigm Dynamic Arrays (BioMark) or OpenArray from Applied Biosystems. The location of Ct values in the plot corresponds to the position of each well on the array.

### Usage

    plotCtArray(q, plot = "Ct", main, col, col.range, na.col = "grey", na.value = 40, chamber.size, ...)

### Arguments

`q` | object of class qPCRset.
`plot` | character string indicating what type of plot to produce. Currently only "Ct" is implemented.
`main` | character string, the title of the plot. Per default "Ct values".
`col` | the name of a colour scheme.
`col.range` | vector, the range of colours to use.
`na.col` | the colour used for well with NA (undetermined) Ct values.
`na.value` | numeric, if NA has been replaced by an (arbitrary) high Ct value in the data.
`chamber.size` | numeric, for adjusting the size of the reaction chamber on the card.
`...` | any other arguments will be passed to the `plot` function.

### Value

A plot is created on the current graphics device.

### Author(s)

Heidi Dvinge

### See Also

`plotCtCard` for plotting data from other high-throughput qPCR platforms.

### Examples

    # Locate example data
    exPath <- system.file("exData", package="HTqPCR")
    exFiles <- "BioMark_sample.csv"
    # Create qPCRset object
    raw <- readCtData(exFiles, path=exPath, n.features=48, n.data=48, format="BioMark")
    # Plot
    plotCtArray(raw)
    # Change colour and range
    plotCtArray(raw, col=brewer.pal(11, "Spectral"), col.range=c(10,35))

[Package HTqPCR version 1.40.0 Index]