image-methods: Method image for objects defined in this package

In maigesPack: Functions to handle cDNA microarray data, including several methods of data analysis

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

x	an object of class maigesRaw, maiges, maigesANOVA, maigesRelNetB, maigesRelNetM, maigesActMod or maigesActNet defined in this package.
name	character string giving a name for sample type tested to be plotted as a name in the method for class maigesRelNetB.
names	similar to the previous one, but it is a vector of length 3 for class maigesRelNetM.
type	string specifying the type of colour map to be plotted. For class maigesActMod it must be 'S' or 'C' for samples or biological conditions, respectively. For class maigesActNet it must be 'score' or 'p-value' for the statistics or p-values of the tests, respectively.
keepEmpty	logical, if true the results of all gene groups are displayed, else only the gene groups that present at least one significant result are displayed.
...	additional arguments for the generic method image from graphics package or maImage defined in package marray (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 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 <[e-mail]>

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)

maigesPack documentation built on Nov. 8, 2020, 6:23 p.m.