qtl (version 1.39-5)

plot.scanPhyloQTL: Plot LOD curves from single-QTL scan to map QTL to a phylogenetic tree

Description

Plot the LOD curves for each partition for a genome scan with a single diallelic QTL (the output of scanPhyloQTL).

Usage

"plot"(x, chr, incl.markers=TRUE, col, xlim, ylim, lwd=2, gap=25, mtick=c("line", "triangle"), show.marker.names=FALSE, alternate.chrid=FALSE, legend=TRUE, ...)

Arguments

x

An object of class "scanPhyloQTL", as output by scanPhyloQTL.

chr

Optional vector indicating the chromosomes to plot. This should be a vector of character strings referring to chromosomes by name; numeric values are converted to strings. Refer to chromosomes with a preceding - to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.

incl.markers

Indicate whether to plot line segments at the marker locations.

col

Optional vector of colors to use for each partition.

xlim

Limits for x-axis (optional).

ylim

Limits for y-axis (optional).

lwd

Line width.

gap

Gap separating chromosomes (in cM).

mtick

Tick mark type for markers (line segments or upward-pointing triangels).

show.marker.names

If TRUE, show the marker names along the x axis.

alternate.chrid

If TRUE and more than one chromosome is plotted, alternate the placement of chromosome axis labels, so that they may be more easily distinguished.

legend

Indicates whether to include a legend in the plot.

...

Passed to the function plot.scanone when it is called.

Value

References

Broman, K. W., Kim, S., An\'e, C. and Payseur, B. A. Mapping quantitative trait loci to a phylogenetic tree. In preparation.

See Also

scanPhyloQTL, max.scanPhyloQTL, summary.scanPhyloQTL, plot.scanone, inferredpartitions, simPhyloQTL, par, colors

Examples

## Not run: 
# # example map; drop X chromosome
# data(map10)           
# map10 <- map10[1:19]
# 
# # simulate data
# x <- simPhyloQTL(4, partition="AB|CD", crosses=c("AB", "AC", "AD"),
#                  map=map10, n.ind=150,
#                  model=c(1, 50, 0.5, 0))
# 
# # run calc.genoprob on each cross
# x <- lapply(x, calc.genoprob, step=2)
# 
# # scan genome, at each position trying all possible partitions
# out <- scanPhyloQTL(x, method="hk")
# 
# # maximum peak
# max(out, format="lod")
# 
# # approximate posterior probabilities at peak
# max(out, format="postprob")
# 
# # all peaks above a threshold for LOD(best) - LOD(2nd best)
# summary(out, threshold=1, format="lod")
# 
# # all peaks above a threshold for LOD(best), showing approx post'r prob
# summary(out, format="postprob", threshold=3)
# 
# # plot of results
# plot(out)
# ## End(Not run)