clines.plot {introgress}R Documentation

Clines Plot

Description

This function produces graphical plots of genomic clines using the output from the function genomic.clines.

Usage

clines.plot(cline.data=NULL,marker.order=NULL,rplots=3,cplots=3,pdf=TRUE,
            out.file="clines.pdf",colors=c("#005A32","#41AB5D"))

Arguments

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.

Details

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. These number of individiuals with each genotype is printed on the right vertical axis. The locus name and P-value are printed in each plot.

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

Value

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

Author(s)

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

References

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.

See Also

genomic.clines

Examples

## 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)

[Package introgress version 1.1 Index]