| corPlot {SLmisc} | R Documentation |
Plot of similarity matrix. This function is a slight modification of function
plot.cor of package "sma".
corPlot(x, new = FALSE, col = grey(0:50/50), minCor, labels = FALSE,
labcols = "black", title = "", protocol = FALSE, cex.axis = 0.8,
cex.axis.bar = 1, ...)
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 |
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). |
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.
Dr. Matthias Kohl (SIRS-Lab GmbH) kohl@sirs-lab.com
Sandrine Dudoit, Yee Hwa (Jean) Yang, Benjamin Milo Bolstad and with
contributions from Natalie Thorne, Ingrid Lönnstedt and Jessica Mar.
sma: Statistical Microarray Analysis.
http://www.stat.berkeley.edu/users/terry/zarray/Html/smacode.html