plotCtBoxes {HTqPCR} | R Documentation

## Boxplots for qPCR Ct values.

### Description

Function for making boxplots of Ct values from high-throughput qPCR data. The boxes can be made either using all values on each card, or stratified by different feature information.

### Usage

    plotCtBoxes(q, cards = TRUE, xlab = "", col, main = NULL, names, stratify = "type", mar = c(7, 4, 3, 1), ...)

### Arguments

`q` | object of class qPCRset.
`cards` | vector, the numbers of the cards to plot. Defaults to TRUE = all cards.
`xlab` | character string, label for the x-axis.
`col` | vector of colours to use, defaults to different colour for each card.
`main` | character string, plot title.
`names` | vector, names to plot under the boxes. Defaults to sample names.
`stratify` | character, specifying what to stratify the Ct values by. NULL, the default means no stratification, "type" is the feature types of the qPCRset, and "class" the feature class.
`mar` | vector, the size of the margins. See `par` for details.
`...` | any other arguments will be passed to the `boxplot` or `par`function.

### Details

For the stratified plots all boxes with Ct values from the same card are plotted in identical colours. "type" and "class" are automatically extracted from the qPCRset using `featureType` and `featureClass`.

### Value

A plot is created on the current graphics device.

### Author(s)

Heidi Dvinge

### See Also

`boxplot`

### Examples

    # Loading the data
    data(qPCRraw)
    # Make plot with all samples or just a few
    plotCtBoxes(qPCRraw, stratify=NULL)
    plotCtBoxes(qPCRraw, cards=c(1,4))
    plotCtBoxes(qPCRraw, stratify="class")

[Package HTqPCR version 1.42.0 Index]