plotMA {limma}R Documentation

MA-Plot

Description

Creates an MA-plot with color coding for control spots.

Usage

plotMA(MA, array=1, xlab="A", ylab="M", main=colnames(MA)[array], xlim=NULL, ylim=NULL, status, values, pch, col, cex, legend=TRUE, zero.weights=FALSE, ...)

Arguments

MA an RGList, MAList or MArrayLM object, or any list with components M containing log-ratios and A containing average intensities. Alternatively a matrix or exprSet object.
array integer giving the array to be plotted. Corresponds to columns of M and A.
xlab character string giving label for x-axis
ylab character string giving label for y-axis
main character string giving title for plot
xlim numeric vector of length 2 giving limits for x-axis, defaults to min and max of the data
ylim numeric vector of length 2 giving limits for y-axis, defaults to min and max of the data
status character vector giving the control status of each spot on the array, of same length as the number of rows of MA$M. If omitted, all points are plotted in the default color, symbol and size.
values character vector giving values of status to be highlighted on the plot. Defaults to unique values of status. Ignored if there is no status vector.
pch vector or list of plotting characters. Default to integer code 16. Ignored is there is no status vector.
col numeric or character vector of colors, of the same length as values. Defaults to 1:length(values). Ignored if there is no status vector.
cex numeric vector of plot symbol expansions, of the the same length as values. Defaults to 0.2 for the most common status value and 1 for the others. Ignored if there is no status vector.
legend logical, should a legend of plotting symbols and colors be included. Ignored if there is no status vector.
zero.weights logical, should spots with zero or negative weights be plotted?
... any other arguments are passed to plot

Details

An MA-plot is a plot of log-intensity ratios (M-values) versus log-intensity averages (A-values). If MA is an RGList or MAList then this function produces an ordinary within-array MA-plot. If MA is an MArrayLM object, then the plot is an fitted model MA-plot in which the estimated coefficient is on the y-axis and the average A-value is on the x-axis.

If MA is a matrix or exprSet object, then this function produces a between-array MA-plot. In this case the A-values in the plot are the average log-intensities across the arrays and the M-values are the deviations of the log-intensities for the specified array from the average. If there are more than five arays, then the average is computed robustly using medians. With five or fewer arrays, it is computed by means.

The status vector is intended to specify the control status of each spot, for example "gene", "ratio control", "house keeping gene", "buffer" and so on. The vector is usually computed using the function controlStatus and a spot-types file. However the function may be used to highlight any subset of spots.

The status can be included as the component MA$genes$Status instead of being passed as an argument to plotMA. The arguments values, pch, col and cex can be included as attributes to status instead of being passed as arguments to plotMA.

See points for possible values for pch, col and cex.

Value

A plot is created on the current graphics device.

Author(s)

Gordon Smyth

References

See http://www.statsci.org/micrarra/refs/maplots.html

See Also

An overview of diagnostic functions available in LIMMA is given in 09.Diagnostics.

Examples

MA <- new("MAList")
MA$A <- runif(300,4,16)
MA$M <- rt(300,df=3)
status <- rep("Gene",300)
status[1:3] <- "M=0"
MA$M[1:3] <- 0
status[4:6] <- "M=3"
MA$M[4:6] <- 3
status[7:9] <- "M=-3"
MA$M[7:9] <- -3
plotMA(MA,main="MA-Plot with Simulated Data",status=status,values=c("M=0","M=3","M=-3"),col=c("blue","red","green"))

#  Same as above
attr(status,"values") <- c("M=0","M=3","M=-3")
attr(status,"col") <- c("blue","red","green")
plotMA(MA,main="MA-Plot with Simulated Data",status=status)

#  Same as above
MA$genes$Status <- status
plotMA(MA,main="MA-Plot with Simulated Data")

[Package limma version 2.4.7 Index]