pcaModels.BigBang {galgo}R Documentation

Plots models in principal components space

Description

Plots models in principal components space.

Usage

## S3 method for class 'BigBang':
pcaModels(O,
        models,
        data=O$data$data,
        traspose=FALSE,
        center=TRUE,
        scale=TRUE,
        subset=NULL,
        main=O$main,
        sampleColors=NULL,
        sampleNames=NULL,
        npc=4,
        pch=19,
        gap=0,
        classes=NULL,
        ...)

Arguments

models The models(chromosomes) to plot. It can be a chromosome list or models resulted from forwardSelectionModel.
data Data if this is not provided in $data$data from the BigBang object.
traspose Traspose the data (for display and data restrictions).
subset To limit the usage of models.
center Logical value indicating whether scalling by genes to mean 0. See prcomp.
scale Logical value indicating whether scalling by genes to 1 variance. See prcomp.
main,gap,pch Plot parameters (method pairs). If pch==NULL, sampleColors are used instead.
sampleColors Colors for samples.
sampleNames To plot the samples names. Use the variable $sampleNames to from the BigBang object.
classes Sample classes. The default is using $classes from bigbang object.
... Other parameters for pairs (or plot) function.

Value

Returns the results of prcomp in a list.

Author(s)

Victor Trevino. Francesco Falciani Group. University of Birmingham, U.K. http://www.bip.bham.ac.uk/bioinf

References

Goldberg, David E. 1989 Genetic Algorithms in Search, Optimization and Machine Learning. Addison-Wesley Pub. Co. ISBN: 0201157675

See Also

For more information see BigBang., *plot(), *forwardSelectionModels(), prcomp(), princomp().

Examples

   #bb is a BigBang object
   pcaModels(bb, bb$bestChromosomes[1])

   fsm <- forwardSelectionModels(bb)
   fsm
   names(fsm)
   heatmapModels(fsm, subset=1)
   fsm <- forwardSelectionModels(bb, minFitness=0.9,
   fitnessFunc=bb$galgo$fitnessFunc)
   heatmapModels(fsm, subset=1)
   pcaModels(fsm, subset=1)
   fitnessSplits(bb, chromosomes=list(fsm$models[[1]]))
[Package galgo version 1.0-10 Index]