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)