plotCtScatter {HTqPCR} | R Documentation

## Scatterplot of two sets of Ct values from qPCR data.

### Description

Produces a plot of Ct values from two samples plotted against each other. Features can be marked based on for example feature class or type.

### Usage

    plotCtScatter(q, cards = c(1, 2), col = "class", pch = 20, diag = FALSE, cor = TRUE, Ct.max = 35, legend = TRUE, ...)

### Arguments

`q` | object of class qPCRset.
`cards` | vector, the two cards to plot against each other.
`col` | vector with the colour(s) to use for the points, or a character string ("type" or "class") indicating whether points should be coloured according to `featureType` or `featureClass` of `q`.
`pch` | integer, the point type to use for the plot.
`diag` | logical, should the diagonal line y=x be plotted.
`cor` | logical, should information about the correlation between the two samples be included in the plot. The correlation is calculated both with and without removing Ct values above Ct.max.
`Ct.max` | numeric, all Ct values above this will be removed for calculating one of the correlations.
`legend` | logical, if `col` is either "type" or "class", should a colour legend for these be included.
`...` | any other arguments are passed to `plot`.

### Value

A figure is generated in the current graphics device.

### Author(s)

Heidi Dvinge

### Examples

    # Load example data
    data(qPCRraw)
    # Various types of plot
    plotCtScatter(qPCRraw, cards=c(1,2))
    plotCtScatter(qPCRraw, cards=c(1,4), col="type")
    plotCtScatter(qPCRraw, cards=c(1,4), col="black", cor=FALSE, diag=TRUE)

[Package HTqPCR version 1.40.0 Index]