plotModel: Plot a QTL model

In qtl: Tools for Analyzing QTL Experiments

Plot a QTL model

Description

Plot a graphical representation of a QTL model, with nodes representing QTL and line segments representing pairwise interactions.

Usage

plotModel(qtl, formula, circrad.rel=0.25, circrad.abs,
         cex.name=1, chronly=FALSE, order, ...)

Arguments

qtl	A QTL object (as created by makeqtl) or vector of character strings indicating the names for the QTL. This is also allowed to be a list that contains a component named "chr" (and, optionally, components names "pos" and "formula").
formula	Optional formula defining the QTL model. If missing, we look for an attribute "formula" to the input QTL object or a item named "formula" within the QTL object.
circrad.rel	Radius of the circles that indicate the QTL, relative to the distance between the circles.
circrad.abs	Optional radius of the circles that indicate the QTL; note that the plotting region will have x- and y-axis limits spanning 3 units.
cex.name	Character expansion for the QTL names.
chronly	If TRUE and a formal QTL object is given, only the chromosome IDs are used to identify the QTL.
order	Optional vector indicating a permutation of the QTL to define where they are to appear in the plot. QTL are placed around a circle, starting at the top and going clockwise.
...	Passed to the function plot.

Value

None.

Author(s)

Karl W Broman, [e-mail]

See Also

stepwiseqtl, makeqtl

Examples

# plot a QTL model, using a vector of character strings to define the QTL
plotModel(c("1","4","6","15"), formula=y~Q1+Q2+Q3*Q4)

# plot an additive QTL model
data(hyper)
hyper <- calc.genoprob(hyper)
qtl <- makeqtl(hyper, chr=c(1,4,6,15), pos=c(68.3,30,60,18), what="prob")
plotModel(qtl)

# include an interaction
plotModel(qtl, formula=y~Q1+Q2+Q3*Q4)

# alternatively, include the formula as an attribute to the QTL object
attr(qtl, "formula") <- y~Q1+Q2+Q3*Q4
plotModel(qtl)

# if formula given, the attribute within the object is ignored
plotModel(qtl, y~Q1+Q2+Q3+Q4)

# NULL formula indicates additive QTL model
plotModel(qtl, NULL)

# reorder the QTL in the figure
plotModel(qtl, order=c(1,3,4,2))

# show just the chromosome numbers
plotModel(qtl, chronly=TRUE)

qtl documentation built on Nov. 28, 2023, 1:09 a.m.