plotDensity {affy} | R Documentation |
Plots the non-parametric density estimates using values contained in the columns of a matrix.
plotDensity(mat, ylab = "density", xlab="x", type="l", col=1:6, na.rm = TRUE, ...) plotDensity.AffyBatch(x, col = 1:6, log = TRUE, which=c("pm","mm","both"), ylab = "density", xlab = NULL, ...)
mat |
A matrix containing the values to make densities in the columns. |
x |
A object of clase AffyBatch |
log |
logical value. If TRUE the log of the intensities in
the AffyBatch are plotted. |
which |
should a histogram of the PMs, MMs, or both be made? |
col |
The colors to use fot the different arrays |
ylab |
a title for the y axis. |
xlab |
a title for the x axis. |
type |
type for the plot. |
na.rm |
handling of NA values. |
... |
graphical parameters can be given as arguments to plot |
The list returned can be convenient for plotting large input matrices with different colors/line types schemes (the computation of the densities can take some time).
To match other functions in base R, this function should probably be
called matdensity
, as it is sharing similarities with
matplot
and matlines
.
It returns invisibly a list of two matrices `x' and `y'.
Ben Bolstad and Laurent Gautier
if (require(affydata)) { data(Dilution) plotDensity(exprs(Dilution), log="x") }