image {maigesPack} | R Documentation

## 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

`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 <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). As we are using as small piece of a large
    ## dataset, this command gives some inconvenient warnings...
    ## Not run:
    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")
    ## End(Not run)

    ## 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)

[Package maigesPack version 1.2.1 Index]