clines.plot: 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 graphical plots of genomic clines using the output from the function genomic.clines.

clines.plot(cline.data=NULL,marker.order=NULL,rplots=3,cplots=3,pdf=TRUE,
            out.file="clines.pdf",colors=c("#005A32","#41AB5D"),
            quantiles=FALSE,lb.cd=rep(0.025,3),ub.cd=rep(0.975,3),
            lb.dh=rep(0.025,2),ub.dh=rep(0.975,2),cd=c("AA","Aa","aa"),dh=c("A","a"))

`cline.data`	a list that is the product of the `genomic.clines` function.
`marker.order`	an optional numeric or character vector specifying the order to plot marker results in; if `marker.order = NULL` markers are plotted in the order they were originally provided.
`rplots`	numerical value specifying the number of plots per row in the output.
`cplots`	numerical value specifying the number of plots per column in the output.
`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.
`quantiles`	logical specifying whether to include genotype specific quantile information on the plots.
`lb.cd`	numeric vector of three proportions specifying the lower bounds for co-dominant markers that is used to determine whether each genotype is under-represented.
`ub.cd`	numeric vector of three proportions specifying the upper bounds for co-dominant markers that is used to determine whether each genotype is over-represented.
`lb.dh`	numeric vector of two proportions specifying the lower bounds for dominant and haploid markers that is used to determine whether each genotype is under-reprsented.
`ub.dh`	numeric vector of two proportions specifying the upper bounds for dominant and haploid markers that is used to determine whether each genotype is over-reprsented.
`cd`	vector with three characters used for labeling genotypes of co-dominant markers in cline plots.
`dh`	vector with two characters used for labeling genotypes of dominant and haploid markers in cline plots.

This function produces graphical plots based on the data object produced by the genomic.clines function. A separate plot is produced for each marker. Plots depict the probability of a given genotype as a function of hybrid index. Plots for the observed data are shown with solid (homozygous population 1 genotype for co-dominant markers, or population 1 allele for dominant or haploid markers) and dashed lines (inter-specific heterozygotes for co-dominant markers, not shown for dominant or haploid markers). If significance testing was conducted with the genomic.clines function, the corresponding 95% confidence intervals are shown in dark and light green. Circles indicate individuals that are homozygous for alleles from population 1 (co-dominant) or population 1 alleles (dominant or haploid) on the top line, interspecific heterozygotes (co-dominant only) in the middle, and homozygotes for alleles from population 2 (co-dominant) or population 2 alleles (dominant or haploid) on the bottom line. The number of individuals with each genotype is printed on the right vertical axis. The locus name and P-value are printed in each plot. If quantiles = TRUE and genotype-specific quantiles were computed with the genomic.clines function by setting classification = TRUE, a title is given for each individual plot that includes whether each genotype (as labeled by cd or dh) was over- (+) or under-represented (-) compared to neutral expectation using lb.cd, ub.cd,lb.dh, ub.dh as thresholds.

See Gompert and Buerkle (2009a, 2009b) for additional details and examples.

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.

Gompert Z. and Buerkle C. A. (2009) introgress: a software package for mapping components of isolation in hybrids. Molecular Ecology Resources, in preparation.

genomic.clines

## 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: 
clines.plot(cline.data=clines.out2)

## End(Not run)