plot.qb.loci {qtlbim} | R Documentation

## Jittered plot of Bayesian QTL loci samples by chromosome

### Description

Each point is one locus from the Bayesian QTL estimates, plotted vertically by chromosome, jittered to give a sense of density. Separate colored vertical bands by loci element.

### Usage

    qb.loci(qbObject, loci = c("main", "epistasis", "GxE"), covar, ...)
    ## S3 method for class 'qb.loci':
    plot(x, loci, labels = FALSE, amount = 0.35, cex, col, ...)
    ## S3 method for class 'qb.loci':
    print(x, ...)
    ## S3 method for class 'qb.loci':
    summary(object, digit = 1, ...)

### Arguments

`qbObject` | Object of class `qb`.
`loci` | Character string identifying MCMC sample elements; may include `"main"`, `"epistasis"`, `"GxE"` and `"all"`.
`covar` | Fixed covariate(s) for `"GxE"` loci; default is all fixed covariates involved in GxE interactions.
`x` | Object of class `qb.loci`.
`object` | Object of class `qb.loci`.
`labels` | Include marker labels if TRUE.
`amount` | Amount of `jitter` (between 0 and .45)
`cex` | Character expansion (may be invisible if too small–default based on number of MCMC samples).
`col` | Character string with colors named by `loci`; also includes color for `marker` lines.
`digit` | Number of digits for roundoff of loci quantiles.
`...` | Graphical parameters can be given as arguments to `plot`. Not used in `qb.loci`.

### Details

Focuses attention on chromosome lengths and concentration of QTL loci estimates. Horizontal lines at markers. Separate bands by `loci` for each chromosome. Adjust `amount` and `cex` to modify look of plot. Most useful when looking at multiple chromosomes.

### Author(s)

Brian S. Yandell, yandell@stat.wisc.edu

### References

http://www.qtlbim.org

### See Also

`jitter`,`subset.qb`

### Examples

    temp <- qb.loci(qbExample)
    plot(temp)
    summary(temp)
    temp <- qb.loci(qbExample, "all")
    plot(temp)
    summary(temp)

[Package qtlbim version 1.6.5 Index]