hist-methods {xps} | R Documentation |
Plot the density estimates for each sample.
Usage
hist(x, which = "", size = 0, transfo = log2, ylab = "density", xlab = "log intensity", type = "l", col = 1:6, ...)
x |
object of class DataTreeSet or ExprTreeSet . |
which |
type of probes to be used, for details see validData . |
size |
length of sequence to be generated as subset. |
transfo |
a valid function to transform the data, usually “log2”, or “0”. |
ylab |
a title for the y axis. |
xlab |
a title for the x axis. |
type |
type for the plot. |
col |
colors to use for the different arrays. |
... |
optional arguments to be passed to plot . |
Plots the non-parametric density estimates using values contained in the columns of
slot data
.
For a DataTreeSet
object, data must first be attached using method
attachInten
.
For exon array raw data only a limited number of samples can be displayed as density plot due to
memory limitations. To display all samples it is proposed to use function root.density
instead.
Christian Stratowa
## load existing ROOT scheme file and ROOT data file scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/")) data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/")) ## need to attach scheme mask and probe intensities data.test3 <- attachMask(data.test3) data.test3 <- attachInten(data.test3) if (interactive()) { hist(data.test3) } ## optionally remove mask and data to free memory data.test3 <- removeInten(data.test3) data.test3 <- removeMask(data.test3)