corPlot: Plot of similarity matrix based on correlation
In MKomics: Omics Data Analysis

Description Usage Arguments Details Value Note Author(s) References Examples

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

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)

`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)`.

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.

invisible()

A first version of this function appeared in package SLmisc.

Matthias Kohl Matthias.Kohl@stamats.de

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

## 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)