| plotModel {qtl} | R Documentation |
Plot a graphical representation of a QTL model, with nodes representing QTL and line segments representing pairwise interactions.
plotModel(qtl, formula, circrad.rel=0.25, circrad.abs,
cex.name=1, chronly=FALSE, order, ...)
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. |
None.
Karl W Broman, kbroman@biostat.wisc.edu
# 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)