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

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.
boxplot(gastro.raw[,1])  ## maigesRaw class, first chip
boxplot(gastro.norm[,8]) ## maigesNorm class, 8th chip
boxplot(gastro.summ[,19]) ## summarized data (also maigesNorm class), 19th chip


## 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")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(maigesPack)
Loading required package: convert
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: marray
Loading required package: graph
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/maigesPack/boxplot-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: boxplot
> ### Title: Method boxplot for objects defined in this package
> ### Aliases: boxplot.maigesRaw boxplot.maiges boxplot.maigesANOVA
> ###   boxplot.maigesDEcluster boxplot
> ### Keywords: array
> 
> ### ** 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.
> boxplot(gastro.raw[,1])  ## maigesRaw class, first chip
> boxplot(gastro.norm[,8]) ## maigesNorm class, 8th chip
> boxplot(gastro.summ[,19]) ## summarized data (also maigesNorm class), 19th chip
> 
> 
> ## 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")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>