boxplot {maigesPack} | R Documentation

## Method boxplot for objects defined in this package

### Description

Generic function `boxplot` to display boxplots of the data.

### Usage

    ## S3 method for class 'maigesRaw':
    boxplot(x, ...)

    ## S3 method for class 'maiges':
    boxplot(x, name=NULL, gLabelID=NULL, sLabelID=NULL, gSamples=NULL, ...)

    ## S3 method for class 'maigesANOVA':
    boxplot(x, name=NULL, gLabelID=NULL, sLabelID=NULL, gSamples=NULL, ...)

    ## S3 method for class 'maigesDEcluster':
    boxplot(x, name=NULL, gLabelID=NULL, sLabelID=NULL, gSamples=NULL, ...)

### Arguments

`x` | an object of any class defined in this package
`name` | character string specifying a gene to do boxplot of their expression values along the types specified by `sLabelID`.
`gLabelID` | character value giving the name of gene label to be used to search for parameter `name`.
`sLabelID` | idem to `gLabelID`, specifying the name of sample label to be used to separate the gene observations.
`gSamples` | a named list containing character vectors defining groups of samples from `sLabelID`.
`...` | additional parameters to `boxplot` method defined in graphics package or to `maBoxplot` method defined in marray package (for `maigesRaw`, `maiges` or `maigesANOVA` classes), in this case the additional parameters must not be named, because these names conflict with the `boxplot` generic function definition.

### Details

This method uses the function `maBoxplot` from marray package to show boxplots of the W values along all the slides of a dataset or along specific accessor methods to stratify the data in objects of class `maigesRaw`. For objects of classes `maiges` or `maigesANOVA` this is also done if the argument `name` is NULL, else the method shows boxplots for the expression values of the gene specified by `name` stratified by sample types from `sLabelID`. For objects of class `maigesDEcluster` only boxplots of genes are produced and the argument `name` may not be NULL.

If you especify the `y` parameter (but not named), defined for the method `maBoxplot` in package marray, it will be displayed the M values instead of W.

### Author(s)

Gustavo H. Esteves <gesteves@vision.ime.usp.br>

### See Also

`maBoxplot` in the marray package and `boxplot` in the graphics package.

### Examples

    ## Loading the dataset
    data(gastro)

    ## To see the boxplots for W values in all chips
    boxplot(gastro.raw)  ## maigesRaw class
    boxplot(gastro.norm) ## maigesNorm class
    boxplot(gastro.summ) ## summarized data (also maigesNorm class)

    ## To see the boxplots for W values in individual chips
    ## separating into print tips. But, as we used only a fraction (500
    ## spots) of the total dataset, this examples doesn't work.
    ## Not run:
    boxplot(gastro.raw[,1])  ## maigesRaw class
    boxplot(gastro.norm[,8]) ## maigesNorm class
    boxplot(gastro.summ[,19]) ## summarized data (also maigesNorm class)
    ## End(Not run)

    ## Boxplot for individual genes into ANOVA model fitting
    gastro.ANOVA = designANOVA(gastro.summ, factors="Tissue")
    gastro.ANOVAfit = deGenesANOVA(gastro.ANOVA, retF=TRUE)

    boxplot(gastro.ANOVAfit, name="KLK13", gLabelID="GeneName",
    sLabelID="Tissue")

[Package maigesPack version 1.2.1 Index]