corplot-methods: Array-Array Expression Level Correlation Plot

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

A heat map of the array-array Spearman rank correlation coefficients.

Usage

corplot(x, which = "UnitName", transfo = log2, method = "spearman", col = NULL, names = "namepart", sort = FALSE, reverse = TRUE, bmar = NULL, add.legend = FALSE, ...)

Arguments

x	object of class ExprTreeSet.
which	type of probes to be used, for details see validData.
transfo	a valid function to transform the data, usually “log2”, or “0”.
method	a character string indicating which correlation coefficient is to be computed.
col	vector of colors for plot, length is number of samples.
names	optional vector of sample names.
sort	logical, if TRUE the correlation matrix will be sorted decreasingly.
reverse	logical, if TRUE the correlation matrix will be replaced by 1 - cor().
bmar	optional list for bottom margin and axis label magnification cex.axis.
add.legend	logical, if TRUE then a color bar will be drawn.
...	optional arguments to be passed to plot.

Details

Produces a heat map of the array-array Spearman rank correlation coefficients for slot data for an object of class ExprTreeSet.

For names=NULL full column names of slot data will be displayed while for names="namepart" column names will be displayed without name extension. If names is a vector of column names, only these columns will displayed as corplot.

For bmar=NULL the default list bmar = list(b=6, cex.axis=1.0) will be used initially. However, both bottom margin and axis label magnification will be adjusted depending on the number of label characters and the number of samples.

Note

Setting reverse = FALSE displays the correlation heat map as in package affyQCReport.

Author(s)

Christian Stratowa

See Also

plotCorr, madplot

xps documentation built on Nov. 8, 2020, 6 p.m.