plotMA.CD: 'MA'-plot for count data.

Description

This function creates an MA-plot from two sets of samples. For those data where the log-ratio is infinite (because in one set of sample data all observed counts are zero), we plot instead the log-values of the other group.

Usage

plotMA.CD(cD, samplesA, samplesB, normaliseData = TRUE, scale = NULL,
xlab = "A", ylab = "M", ...)

Arguments

A countData object.

samplesA

Either a character vector, identifying sample set A by either replicate name or sample name, or a numerical vector giving the columns of data in the 'countData' object that forms sample set A. See Details.

samplesB

Either a character vector, identifying sample set B by either replicate name or sample name, or a numerical vector giving the columns of data in the 'countData' object that forms sample set B. See Details.

normaliseData

Should the data be normalised by library size before computing log-ratios? Defaults to TRUE.

scale

If given, defines the scale on which the log-ratios will be plotted. Defaults to NULL, implying that the scale will be calculated by the function.

xlab

Label for the X-axis. Defaults to "A".

ylab

Label for the Y-axis. Defaults to "M".

...

Any other parameters to be passed to the plot function.

Value

Plotting function.

Details

The samples sets can be identified either by a numeric vector which specifies the columns of data from the countData object 'cD', or by a character vector. If a character vector is used, the members of the character vector will first be searched for in the @replicates slot of the 'cD' object. Any members of the vector not found in the replicates slot, will be searched for in the column names of the @data slot of the 'cD' object. Different classes of vector can be used for 'samplesA' and 'samplesB', as shown in the example below.

Examples

Run this code

data(simData)

replicates <- c("simA", "simA", "simA", "simA", "simA", "simB", "simB", "simB", "simB", "simB")
groups <- list(NDE = c(1,1,1,1,1,1,1,1,1,1), DE = c(1,1,1,1,1,2,2,2,2,2))
CD <- new("countData", data = simData, replicates = replicates, groups = groups)

#estimate library sizes for countData object
libsizes(CD) <- getLibsizes(CD)

#MA-plot comparing replicate groups
plotMA.CD(CD, samplesA = "simA", samplesB = 6:10)