R: Plot a QTL model

plotModel {qtl} | R Documentation

## 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, kbroman@biostat.wisc.edu

### 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)

[Package qtl version 1.41-6 Index]