madPlot {MKomics} | R Documentation |
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
x |
data or correlation matrix, respectively |
new |
If |
col |
colors palette for image. If missing, the |
maxMAD |
maximum MAD value displayed |
labels |
vector of character strings to be placed at the tickpoints,
labels for the columns of |
labcols |
colors to be used for the labels of the columns of |
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 |
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 Matthias.Kohl@stamats.de
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)