| pmplot-methods {xps} | R Documentation |
Creates a barplot of mean perfect match and mismatch intensities.
Usage
pmplot(x, which = "", size = 0, transfo = NULL, method = "mean", names = "namepart", beside = TRUE, col = c("red", "blue"), legend = c("PM","MM"), ...)
x |
object of class DataTreeSet. |
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”. |
method |
method to compute average intensities, “mean” or “median”. |
names |
optional vector of sample names. |
beside |
logical. If FALSE, mean intensities are portrayed as stacked bars,
and if TRUE the columns are portrayed as juxtaposed bars. |
col |
color of PM, MM bars. |
legend |
a vector of text used to construct a legend for the plot, or a logical indicating whether a legend should be included. |
... |
optional arguments to be passed to barplot. |
Produces barplots of mean perfect match and mismatch intensities for slot data
for an object of class 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 pmplot.
Data must first be attached to class DataTreeSet 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()) {
pmplot(data.test3)
}
## optionally remove mask and data to free memory
data.test3 <- removeInten(data.test3)
data.test3 <- removeMask(data.test3)