madPlot: Plot of similarity matrix based on MAD

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

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.

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

Examples

Run this code

# NOT RUN {
## 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)
# }