R: Heatmap of a genome of MQM scan on multiple phenotypes

mqmplot.heatmap {qtl} | R Documentation

## Heatmap of a genome of MQM scan on multiple phenotypes

### Description

Plotting routine to display a heatmap of results obtained from a multiple-QTL model on multiple phenotypes (the output of `mqmscanall`)

### Usage

    mqmplot.heatmap(cross, result, directed=TRUE, legend=FALSE, breaks =
    c(-100,-10,-3,0,3,10,100), col =
    c("darkblue","blue","lightblue","yellow","orange","red"), ...)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`result` | Result object from mqmscanall, the object needs to be of class `mqmmulti`
`directed` | Take direction of QTLs into account (takes more time because of QTL direction calculations
`legend` | If TRUE, add a legend to the plot
`breaks` | Color break points for the LOD scores
`col` | Colors used between breaks
`...` | Additional arguments passed to the `image` function

### Author(s)

Danny Arends danny.arends@gmail.com

### See Also

- The MQM tutorial: https://rqtl.org/tutorials/MQM-tour.pdf

- `MQM` - MQM description and references

- `mqmscan` - Main MQM single trait analysis

- `mqmscanall` - Parallellized traits analysis

- `mqmaugment` - Augmentation routine for estimating missing data

- `mqmautocofactors` - Set cofactors using marker density

- `mqmsetcofactors` - Set cofactors at fixed locations

- `mqmpermutation` - Estimate significance levels

- `scanone` - Single QTL scanning

### Examples

    data(multitrait)

    multitrait <- fill.geno(multitrait) # impute missing genotype data
    result <- mqmscanall(multitrait, logtransform=TRUE)
    mqmplot.heatmap(multitrait,result)

[Package qtl version 1.46-2 Index]