R: Wrapper function which calls various visualization methods for expression data

doPlots {StabPerf}

R Documentation

Wrapper function which calls various visualization methods for expression data

Description

Runs the plot functions: customBoxplot, doQuantplot, dopValueplot, doVolcanoplot for a given data set and saves them all in graphics files via save.plot.

Usage

doPlots(data, labels, quantplot_range=NULL, boxplot_range=NULL,
 prefix="", foldChanges=NULL, pValues=NULL)

Arguments

`data`	data.frame or matrix. Expression values, with the samples in the columns.
`labels`	factor. Classes of the samples in `data`
`quantplot_range`	See `doQuantplot`
`boxplot_range`	See `customBoxplot`
`prefix`	See `save.plot`
`foldChanges`	numeric. Multi-way array of fold changes.
`pVaues`	numeric. Multi-way array of fold changes.

Details

A multi-way array here means: if labels contains four unique classes, then foldChanges and pValues are 4x4xN arrays, whereby N is the length of the data vectors (columns) in data.

If there are more than two classes in labels then the p-value and volcano plots are performed for all pair-wise combinations of classes in labels.

Examples

# Provide p-values and fold-changes to get p-value and volcano plots
# Otherwise only boxplots and quantile plots are produced
doPlots(data, factors, prefix="round1", foldChanges, pValues)