plotCtArray: Image plot of qPCR Ct values from an array format

Description Usage Arguments Value Author(s) See Also Examples

View source: R/plotCtArray.R

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

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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numeric, if NA has been replaced by an (arbitrary) high Ct value in the data.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

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# 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))

HTqPCR documentation built on Nov. 1, 2018, 2:23 a.m.