qtl.heatmap: Plot a Heatmap of all QTL

In dmgatti/DOQTL: Genotyping and QTL Mapping in DO Mice

Plot a Heatmap of all QTL

Description

This function accepts LOD scores and SNP locations and plots a heatmap of the QTL. Each QTL is scaled to between 0 and 1 and the QTL are hierarchically clustered. A tile plot is then created with QTL colored from white (strong) to black (weak). The motivation for this plot is to visualize QTL that may be coincident across different phenotypes.

Usage

  qtl.heatmap(lod, ...)

Arguments

lod	Data frame, containing the SNP names, chromosome an dbp locations in columns 1 through 3 and LOD scores for all phenotyped in the remaining columns.
...	Additional arguments to be passed to plot.

Value

No value is returned. A tile plot is plotted from the data.

Note

The QTL the appear in white are *not* neccessarily signficant. They are simply the strongest QTL for each phenotype.

Author(s)

Daniel Gatti

See Also

plot.doqtl, scanone, scanone.perm

Examples

  ## Not run: 
    qtl.heatmap(lod)
  
## End(Not run)

dmgatti/DOQTL documentation built on April 7, 2024, 10:35 p.m.