composite.clines: Composite Clines Plot
In introgress: methods for analyzing introgression between divergent lineages

Description Usage Arguments Details Value Author(s) References See Also Examples

This function produces an overlayed graphical plot of genomic clines using the output from the function genomic.clines.

1 2	composite.clines(cline.data=NULL,pdf=TRUE,out.file="comp.pdf", colors=c("#005A32","#41AB5D"),labels=c("AA","Aa"))

`cline.data`	a list that is the product of the `genomic.clines` function.
`pdf`	logical specifying whether to print the plots to a pdf file; if `pdf=FALSE` plots are printed to the current graphical device.
`out.file`	a character string for the filename for the output if `pdf=TRUE`.
`colors`	a vector of two colors to be used for cline plots.
`labels`	vector with two characters used for labeling marker genotypes on the plots.

This function produces graphical plots based on the data object produced by the genomic.clines function. Plots depict the probability of a given genotype as a function of hybrid index. Unlike the clines.plot function, plots for each marker are overlayed. If significance testing was performed the null distribution of the first marker is shown (which should be the same as the null distribution for all markers if the permutation method was used). This function only works with co-dominant markers. See Teeter et al. 2010 for an example of the plot produced by this function. Also, compare this function to clines.plot.

A plot is produced, but a data object is not returned.

Zachariah Gompert zgompert@uwyo.edu, C. Alex Buerkle buerkle@uwyo.edu

Gompert Z. and Buerkle C. A. (2009) A powerful regression-based method for admixture mapping of isolation across the genome of hybrids. Molecular Ecology, 18, 1207-1224.

Teeter K. C., Thibodeau L. M., Gompert Z., Buerkle C. A., Nachman M. W., and Tucker, P. K. (2010) The variable genomic architecture of isolation between hybridizing species of house mice. Evolution, 64, 472-485.

genomic.clines, clines.plot

## this code assumes the data object clines.out2 has been produced using
## the sample code for the "genomic.clines" function

## produce plots of genomic clines 
## Not run: 
composite.clines(cline.data=clines.out2)

## End(Not run)