galgo (version 1.4)

pcaModels.BigBang: Plots models in principal components space

Description

Plots models in principal components space.

Usage

# S3 method for 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=0.25,
	classes=NULL,
    show.loadings=FALSE,
    loadings.round=6,
    labels=TRUE,
    order=0,
    col=1:200,
    columns=NULL,
    jitterFactor=0,
	...)

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.

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

# NOT RUN {
   #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]]))
   
# }
# NOT RUN {
 
# }