corPlot {MKomics}

Plot of similarity matrix based on correlation

Description

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

Usage

corPlot(x, new = FALSE, col, minCor, 
        labels = FALSE, lab.both.axes = FALSE, labcols = "black", 
        title = "", cex.title = 1.2, 
        protocol = FALSE, cex.axis = 0.8, 
        cex.axis.bar = 1, signifBar = 2, ...)
        
corPlot2(x, new = FALSE, col, minCor = 0.5, labels = FALSE, 
         row.width = 6, column.height = 6, lab.both.axes = TRUE, 
         fontsize.axis = 12, title = "", fontsize.title = 16, 
         signifBar = 2)

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.

lab.both.axes

logical, display labels on both axes

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.

cex.title

numerical value giving the amount by which plotting text and symbols should be magnified relative to the default; cf. par, cex.main.

fontsize.title

numerical value giving the fontsize of the title.

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.

fontsize.axis

numerical value giving the fontsize of the axis labels.

cex.axis.bar

The magnification to be used for axis annotation of the color bar relative to the current setting of 'cex'; cf. par.

signifBar

integer indicating the precision to be used for the bar.

row.width

numerical value giving width of the row in centimeters; i.e., can be used to change space available for the labels.

column.height

numerical value giving the height of the column in centimeters; i.e., can be used to change space available for the labels.

...

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 [e-mail]

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/Software/smacode.html

Examples

## only a dummy example
M <- matrix(rnorm(1000), ncol = 20)
colnames(M) <- paste("Sample", 1:20)
M.cor <- cor(M)

corPlot(M.cor, minCor = min(M.cor))
corPlot(M.cor, minCor = min(M.cor), lab.both.axes = TRUE)
corPlot(M.cor, minCor = min(M.cor), protocol = TRUE)
corPlot(M.cor, minCor = min(M.cor), signifBar = 1)

corPlot2(M.cor, minCor = min(M.cor))
corPlot2(M.cor, minCor = min(M.cor), lab.both.axes = FALSE)
corPlot2(M.cor, minCor = min(M.cor), signifBar = 1)