Scatterplot of two sets of Ct values from qPCR data.

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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

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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

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# 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)

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