boxplot-methods {xps} | R Documentation |
Produce box-and-whisker plot(s) of the samples.
Usage
boxplot(x, which = "", size = 0, transfo = log2, range = 0, names = "namepart", ...)
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”. |
range |
determines how far the plot whiskers extend out from the box. |
names |
optional vector of sample names. |
... |
optional arguments to be passed to boxplot . |
Creates a boxplot for slot data
for an object of class DataTreeSet
or ExprTreeSet
.
For names=NULL
full column names of slot data
will be displayed while for
names="namepart"
column names will be displayed without name extension. If names
is a vector of column names, only these columns will displayed as boxplot.
For a DataTreeSet
object, data must first be attached using method
attachInten
.
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()) { boxplot(data.test3) } ## optionally remove mask and data to free memory data.test3 <- removeInten(data.test3) data.test3 <- removeMask(data.test3) rm(scheme.test3, data.test3) gc()