xps (version 1.32.0)

plotCorr: Array-Array Expression Level Correlation Plot for Device

Description

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

Usage

plotCorr(x, which      = "UnitName", transfo    = log2, method     = "spearman", col        = NULL, names      = "namepart", sort       = FALSE, reverse    = TRUE, bmar       = NULL, add.legend = FALSE, dev        = "screen", outfile    = "CorrelationPlot", w          = 540, h          = 540, ...)

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.

dev

graphics device to plot to, i.e. one of “screen”, “jpeg”,“png”, “pdf” or “ps”.

outfile

the name of the output file.

w

the width of the device in pixels.

h

the height of the device in pixels.

...

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.

See Also

corplot