pmplot-methods {xps} | R Documentation

## Barplot of PM and MM Intensities.

### Description

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"), ...)`

### Arguments

`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`.

### Details

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.

### Note

Data must first be attached to class `DataTreeSet` using method `attachInten`.

### Author(s)

Christian Stratowa

### See Also

`boxplot.dev`, `boxplot`, `barplot`

### Examples

    ## 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)

[Package xps version 1.4.10 Index]