heatmapModels.BigBang: Plots models using heatmap plot

In galgo: Genetic Algorithms for Multivariate Statistical Models from Large-Scale Functional Genomics Data

Description

Plots models using heatmap plot.

Usage

## S3 method for class 'BigBang'
heatmapModels(	O, 
	models, 
	data=O$data$data, 
	geneNames=paste(pad(1:length(O$geneNames), char="  ")," : ",O$geneNames,sep=""),
	traspose=TRUE, 
	subset=NULL, 
	main=O$main, 
	scale=if (traspose) "column" else "row", 
	col=c(rgb(0,8:0/8,0),rgb(1:8/8,0,0)), 
	RowSideColors=NULL, 
	ColSideColors=NULL,
	hclustfun=function(x) hclust(x, method="ward"),
    distfun = dist,
	histscale=1,
	nc=NULL,
    byclasscolor=FALSE,
    Colv=NULL,
    Rowv=NULL,
    heatmapfunc=heatmap,
    use.ranks=FALSE,
    columns=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.
geneNames	Names for the genes. The default uses the $geneNames from BigBang object.
traspose	Traspose the data (for display and data restrictions).
subset	To limit the usage of models.
scale,col,RowSideColors,ColSideColors	Heatmap parameters. Provided for compatibility. If col is -1,-2,-3, or -4, standard microarray colors are used. If length(col)==3, these three colours are used to build a gradient.
geneColors	A list of specific RowSideColors parameter for every model.
sampleColors	Colors for samples.
hclustfun	Function to heatmap. The default use “ward” method. Use hclustfun=hclust to restore the original heatmap behaviour.
...	Other parameters for heatmap function.

Value

Returns nothing.

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(), heatmap().

Examples

## Not run: 
   #bb is a BigBang object
   heatmapModels(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]]))
   
## End(Not run)
 

galgo documentation built on May 2, 2019, 4:20 a.m.