corPlot {MKmisc}R Documentation

Plot of similarity matrix based on correlation

Description

Plot of similarity matrix. This function is a slight modification of function plot.cor of package "sma".

Usage

corPlot(x, new = FALSE, col, minCor, labels = FALSE, 
          labcols = "black", title = "", protocol = FALSE, cex.axis = 0.8, 
          cex.axis.bar = 1, ...)

Arguments

x data or correlation matrix, respectively
new If new=FALSE, x must already be a correlation matrix. If new=TRUE, the correlation matrix for the columns of x is computed and displayed in the image.
col colors palette for image. If missing, the RdYlGn palette of RColorBrewer is used.
minCor numeric value in [-1,1], used to adjust col
labels vector of character strings to be placed at the tickpoints, labels for the columns of x.
labcols colors to be used for the labels of the columns of x. labcols can have either length 1, in which case all the labels are displayed using the same color, or the same length as labels, in which case a color is specified for the label of each column of x.
title character string, overall title for the plot.
protocol logical, display color bar without numbers
cex.axis The magnification to be used for axis annotation relative to the current setting of 'cex'; cf. par.
cex.axis.bar The magnification to be used for axis annotation of the color bar relative to the current setting of 'cex'; cf. par.
... graphical parameters may also be supplied as arguments to the function (see par). For comparison purposes, it is good to set zlim=c(-1,1).

Details

This functions generates the so called similarity matrix (based on correlation) for a microarray experiment.

If min(x), respectively min(cor(x)) is smaller than minCor, the colors in col are adjusted such that the minimum correlation value which is color coded is equal to minCor.

Value

invisible()

Note

A first version of this function appeared in package SLmisc.

Author(s)

Matthias Kohl Matthias.Kohl@stamats.de

References

Sandrine Dudoit, Yee Hwa (Jean) Yang, Benjamin Milo Bolstad and with contributions from Natalie Thorne, Ingrid Loennstedt and Jessica Mar. sma: Statistical Microarray Analysis.
http://www.stat.berkeley.edu/users/terry/zarray/Html/smacode.html

See Also

plot.cor

Examples

## only a dummy example
M <- cor(matrix(rnorm(1000), ncol = 20))
corPlot(M, minCor = min(M))

[Package MKmisc version 0.3 Index]