madPlot: Plot of similarity matrix based on MAD

In MKomics: Omics Data Analysis

Description

Plot of similarity matrix based on MAD between microarrays.

Usage

madPlot(x, new = FALSE, col, maxMAD = 3, labels = FALSE, 
        labcols = "black", title = "", protocol = FALSE, ...)

madPlot2(x, new = FALSE, col, maxMAD = 3, 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 matrix with MAD values. If new=TRUE, the MAD 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.
maxMAD	maximum MAD value displayed
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.
fontsize.title	numerical value giving the fontsize of the title.
protocol	logical, display color bar without numbers
lab.both.axes	logical, display labels on both axes
fontsize.axis	numerical value giving the fontsize of the axis labels.
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 MAD) for a microarray experiment; cf. Buness et. al. (2004). The function is similar to corPlot.

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

Andreas Buness, Wolfgang Huber, Klaus Steiner, Holger Sueltmann, and Annemarie Poustka. arrayMagic: two-colour cDNA microarray quality control and preprocessing. Bioinformatics Advance Access published on September 28, 2004. doi:10.1093/bioinformatics/bti052

See Also

corPlot

Examples

## only a dummy example
set.seed(13)
x <- matrix(rnorm(1000), ncol = 10)
x[1:20,5] <- x[1:20,5] + 10
madPlot(x, new = TRUE, maxMAD = 2.5)
madPlot2(x, new = TRUE, maxMAD = 2.5)
## in contrast
corPlot2(x, new = TRUE, minCor = -0.5)

MKomics documentation built on Aug. 8, 2021, 5:06 p.m.