plot.World: Plots information about world object

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

Description

Plot assumes that the World object contains only Niches objects. See arguments for details.

Usage

## S3 method for class 'World'
plot(x,
	type=c("chromosomes", "fitness"),
	horiz=TRUE,
	pch=19,
	col=1,
	main="",
	xlab="",
	ylab="",
	chromosome=NULL,
	chromosome.chr="U",
	...)

Arguments

type	The type of plot. "chromosomes" will plot the chromosomes in one axis and the genes in the other axis. The maximum chromosome is drawn with "M", the best chromosome with "B" and the user chromosome with "U". This plot give an overview of the population coverage. "fitness" plot the current fitness in vertical axis against chromosome index in horizontal.
horiz	Exchange the default choice of axis when type="chromosomes".
main,xlab, ylab,col,pch	World defaults for common plot parameters. Their usage overwrite the default value. col controls the color for chromosomes
chromosome	An additional chromosome for comparison.
chromosome.chr	Explicit character for additional chromosome.
chromosomes	Use the specific list of chromosomes instead of the original Niche chromosomes.
...	Other user named values to include in the object.

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 World.

Examples

   cr <- Chromosome(genes=newCollection(Gene(shape1=1, shape2=100),5))
   ni <- Niche(chromosomes=newRandomCollection(cr, 10))
   ni$fitness <- runif(10)  ## tricky fitness
   ni
   wo <- World(niches=newRandomCollection(ni,2))
   refreshStats(wo)
   plot(wo, main="My Niche")
   plot(wo, type="fitness")
 

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