R: Plot LOD curves from single-QTL scan to map QTL to a...

plot.scanPhyloQTL {qtl} | R Documentation

## 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

    ## S3 method for class 'scanPhyloQTL'
    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

None.

### Author(s)

Karl W Broman, broman@wisc.edu

### 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)

[Package qtl version 1.46-2 Index]