clines.plot {introgress} | R Documentation |
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.
## 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)