plotMDS: Multidimensional scaling plot of microarray data

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

Description

Plot the sample relations based on MDS. Distances on the plot can be interpreted in terms of leading log2-fold-change.

Usage

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## Default S3 method:
plotMDS(x, top=500, labels=colnames(x), col=NULL, cex=1, dim.plot=c(1,2), ndim=max(dim.plot), gene.selection="pairwise",
        xlab=paste("Dimension",dim.plot[1]), ylab=paste("Dimension",dim.plot[2]), ...)
## S3 method for class 'MDS'
plotMDS(x, labels=colnames(x$distance.matrix), col=NULL, cex=1, dim.plot=x$dim.plot, xlab=paste("Dimension",dim.plot[1]), ylab=paste("Dimension",dim.plot[2]),...)

Arguments

x

any data object which can be coerced to a matrix, such as ExpressionSet or EList.

top

number of top genes used to calculate pairwise distances.

labels

character vector of sample names or labels. If x has no column names, then defaults the index of the samples.

col

numeric or character vector of colors for the plotting characters.

cex

numeric vector of plot symbol expansions.

dim.plot

which two dimensions should be plotted, numeric vector of length two.

ndim

number of dimensions in which data is to be represented

gene.selection

character, "pairwise" to choose the top genes separately for each pairwise comparison between the samples or "common" to select the same genes for all comparisons

xlab

title for the x-axis

ylab

title for the y-axis

...

any other arguments are passed to plot.

Details

This function is a variation on the usual multdimensional scaling (or principle coordinate) plot, in that a distance measure particularly appropriate for the microarray context is used. The distance between each pair of samples (columns) is the root-mean-square deviation (Euclidean distance) for the top top genes. Distances on the plot can be interpreted as leading log2-fold-change, meaning the typical (root-mean-square) log2-fold-change between the samples for the genes that distinguish those samples.

If gene.selection is "common", then the top genes are those with the largest standard deviations between samples. If gene.selection is "pairwise", then a different set of top genes is selected for each pair of samples. The pairwise feature selection may be appropriate for microarray data when different molecular pathways are relevant for distinguishing different pairs of samples.

See text for possible values for col and cex.

Value

A plot is created on the current graphics device.

An object of class "MDS" is invisibly returned. This is a list containing the following components:

distance.matrix

numeric matrix of pairwise distances between columns of x

cmdscale.out

output from the function cmdscale given the distance matrix

dim.plot

dimensions plotted

x

x-xordinates of plotted points

y

y-cordinates of plotted points

gene.selection

gene selection method

Author(s)

Di Wu and Gordon Smyth

See Also

cmdscale

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

Examples

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# Simulate gene expression data for 1000 probes and 6 microarrays.
# Samples are in two groups
# First 50 probes are differentially expressed in second group
sd <- 0.3*sqrt(4/rchisq(1000,df=4))
x <- matrix(rnorm(1000*6,sd=sd),1000,6)
rownames(x) <- paste("Gene",1:1000)
x[1:50,4:6] <- x[1:50,4:6] + 2
# without labels, indexes of samples are plotted.
mds <- plotMDS(x,  col=c(rep("black",3), rep("red",3)) )
# or labels can be provided, here group indicators:
plotMDS(mds,  col=c(rep("black",3), rep("red",3)), labels= c(rep("Grp1",3), rep("Grp2",3)))

richierocks/limma2 documentation built on May 27, 2019, 8:47 a.m.