mqmplot.clusteredheatmap {qtl}R Documentation

Plot clustered heatmap of MQM scan on multiple phenotypes

Description

Plot the results from a MQM scan on multiple phenotypes.

Usage

mqmplot.clusteredheatmap(cross, mqmresult, directed=TRUE, legend=FALSE, Colv=NA, scale="none", verbose=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.
mqmresult 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
Colv Cluster only the Rows, the columns (Markers) should not be clustered
scale character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. The default "none"
verbose If TRUE, give verbose output.
breaks Color break points for the LOD scores
col Colors used between breaks
... Additional arguments passed to heatmap.

Author(s)

Danny Arends danny.arends@gmail.com

See Also

Examples

data(multitrait)

multitrait <- fill.geno(multitrait) # impute missing genotype data
result <- mqmscanall(multitrait, logtransform=TRUE)
cresults <- mqmplot.clusteredheatmap(multitrait,result)
groupclusteredheatmap(multitrait,cresults,10)

[Package qtl version 1.21-2 Index]