Method image for objects defined in this package

Description

Generic function image to display colour maps of numerical values stored in objects defined in this package.

Usage

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

## S3 method for class 'maiges'
image(x, ...)

## S3 method for class 'maigesANOVA'
image(x, ...)

## S3 method for class 'maigesRelNetB'
image(x=NULL, name=NULL, ...)

## S3 method for class 'maigesRelNetM'
image(x=NULL, names=NULL, ...)

## S3 method for class 'maigesActMod'
image(x, type=c("S","C")[2], keepEmpty=FALSE, ...)

## S3 method for class 'maigesActNet'
image(x, type=c("score","p-value")[1], ...)

Arguments

Details

This method uses the function maImage from marray package to display colour maps of accessor methods defined into marray package for objects of class maiges or maigesRaw and maigesANOVA.

For objects of class maigesRelNetM the method displays 3 colour maps representing the correlation values for the two groups tested and the p-values of the tests.

For class maigesRelNetB it displays the correlation values for the type tested.

In objects of class maigesActMod it displays the fraction of genes induced or repressed for each gene group, by samples or biological type.

Finally, for class maigesActNet, the method display the matrix of statistics or p-values of the tests.

Pay attention, if you specify the parameter x (but not named) for maImage) it will plot the M values instead of W (default).

Author(s)

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

See Also

image in the graphics package and maImage in marray package.

Examples

## Loading the dataset
data(gastro)

## Doing image plots (using package marray), default method showing the
## W values (for 1st chip), after showing the A values (2nd chip) and
## red background (20th chip).
image(gastro.raw[,1])
image(gastro.raw[,2], "maA")
image(gastro.raw[,20], "maRb")

## Example for normalized objects (showing A values for the 5th chip).
image(gastro.norm[,5], "maA")



## Example for object of class maigesRelNetB

## Constructing the relevance network (Butte's method) for sample
## 'Tissue' equal to 'Neso' for the 1st gene group
gastro.net = relNetworkB(gastro.summ, sLabelID="Tissue", 
  samples="Neso", geneGrp=1, type="Rpearson")

image(gastro.net)




## Example for object of class maigesRelNetM

## Constructing the relevance network for sample
## 'Tissue' comparing 'Neso' and 'Aeso' for the 1st gene group
gastro.net = relNetworkM(gastro.summ, sLabelID="Tissue", 
  samples = list(Neso="Neso", Aeso="Aeso"), geneGrp=11,
  type="Rpearson")

image(gastro.net)

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/image-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: image
> ### Title: Method image for objects defined in this package
> ### Aliases: image.maigesRaw image.maiges image.maigesANOVA
> ###   image.maigesRelNetB image.maigesRelNetM image.maigesActMod
> ###   image.maigesActNet image
> ### Keywords: array
> 
> ### ** Examples
> 
> ## Loading the dataset
> data(gastro)
> 
> ## Doing image plots (using package marray), default method showing the
> ## W values (for 1st chip), after showing the A values (2nd chip) and
> ## red background (20th chip).
> image(gastro.raw[,1])
[1] FALSE
NULL
> image(gastro.raw[,2], "maA")
[1] FALSE
NULL
> image(gastro.raw[,20], "maRb")
[1] FALSE
NULL
> 
> ## Example for normalized objects (showing A values for the 5th chip).
> image(gastro.norm[,5], "maA")
[1] FALSE
NULL
> 
> 
> 
> ## Example for object of class maigesRelNetB
> 
> ## Constructing the relevance network (Butte's method) for sample
> ## 'Tissue' equal to 'Neso' for the 1st gene group
> gastro.net = relNetworkB(gastro.summ, sLabelID="Tissue", 
+   samples="Neso", geneGrp=1, type="Rpearson")
> 
> image(gastro.net)
> 
> 
> 
> 
> ## Example for object of class maigesRelNetM
> 
> ## Constructing the relevance network for sample
> ## 'Tissue' comparing 'Neso' and 'Aeso' for the 1st gene group
> gastro.net = relNetworkM(gastro.summ, sLabelID="Tissue", 
+   samples = list(Neso="Neso", Aeso="Aeso"), geneGrp=11,
+   type="Rpearson")
> 
> image(gastro.net)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>