plotCtCard: Image plot of qPCR Ct values from a card format

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/plotCtCard.R

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

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numeric, if NA has been replaced by an (arbitrary) high Ct value in the data.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

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# 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")

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