plotCtCard {HTqPCR} | R Documentation

## Image plot of qPCR Ct values from a card format

### Description

Function for plotting high-throughput qPCR Ct values from a platform with a defined spatial layout, such as TaqMan Low Density Assay cards. The location of Ct values in the plot corresponds to the position of each well on the card.

### Usage

    plotCtCard(q, card = 1, plot = "Ct", main, nrow = 16, ncol = 24, col, col.range, na.col = "grey", na.value = 40, legend.cols, well.size = 3.1, zero.center = FALSE, unR = FALSE, unD = FALSE, ...)

### Arguments

`q` | object of class qPCRset.
`card` | integer, the sample number to plot.
`plot` | character string among "Ct", "flag", "type", "class") indicating what type of plot to produce. See Details for a longer description.
`main` | character string, the title of the plot. Per deault this is the sample name corresponding to card.
`nrow` | integer, the numer of rows on the card (16 for a standard 384 well format).
`ncol` | integer, the numer of columns on the card (24 for a standard 384 well format).
`col` | vector of colors of the same length as the number of different groups for the categorical data, or the name of a colour scheme for the continuous data.
`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`na.value` | numeric, if NA has been replaced by an (arbitrary) high Ct value in the data.
`legend.cols` | integer, how many columns should the legend text be split into (defaults to number of labels).
`well.size` | numeric, for adjusting the size of the wells on the card.
`zero.center` | logical, should the colours be shifted to be zero-centered.
`unR` | logical, should wells from the category "Unreliable" be crossed out.
`unD` | logical, should wells from the category "Undetermined" be crossed out.
`...` | any other arguments will be passed to the `plot` and `points` functions.

### Details

This function may be used to plot the values of any well-specific information, such as the raw or normalized Ct values, or categorical data such as flag, gene class etc. The image follows the layout of an actual HTqPCR card.

If `unR=TRUE` these will wells will be crossed out using a diagonal cross (X), whereas `unD=TRUE` will be marked with a horisontal/vertical cross.

### Value

A plot is created on the current graphics device.

### Author(s)

Heidi Dvinge

### See Also

`image`, and `plotCtArray` for plotting data from other high-throughput qPCR platforms (e.g. Fluidigm arrays).

### Examples

    # Load some example data
    data(qPCRraw)
    # Plot Ct values from first card
    plotCtCard(qPCRraw)
    plotCtCard(qPCRraw, card=2, col.range=c(10,35))
    plotCtCard(qPCRraw, unR=TRUE, unD=TRUE)
    # Other examples
    plotCtCard(qPCRraw, plot="class")
    plotCtCard(qPCRraw, plot="type")
    plotCtCard(qPCRraw, plot="flag")

[Package HTqPCR version 1.40.0 Index]