heatMap {ASMap}

Heat map of the estimated pairwise recombination fractions and LOD linkage between markers.

Description

Heat map of the estimated pairwise recombination fractions and LOD linkage between markers that provides extended functionality of Bromans qtl package plotRF function.

Usage

heatMap(x, chr, mark, what = c("both", "lod", "rf"), lmax = 12,
   rmin = 0, markDiagonal = FALSE, color =
rev(colorRampPalette(brewer.pal(11,"Spectral"))(256)),  ...)

Arguments

x

A "cross" object generated from the qtl package.

chr

A character string of linkage group names to subset the cross object.

mark

An argument to subset linkage groups further into marker subsets. This can be a single numerical vector of markers positions which will subset all linkage groups in the same manner. Or it may be a list of numerical vectors named by the linkage group names with which to subset the linkage groups separately.

what

A character string of either "lod", "rf" or "both". If "lod" only pairwise LOD scores between markers are plotted. If "rf" then only pairwise recombination fractions between markers are plotted. If "both" then both are plotted with LOD on the lower triangle and recombination in the upper triangle. This is the default (see Details).

lmax

The threshold LOD score to implemented. Scores above this threshold will be plotted at the same colour.

rmin

The threshold recombination fraction to be implemented. Recombination fractions below this threshold will be plotted at the same colour.

markDiagonal

Logical value. If TRUE then borders are added around the diagonal elements of the heat map.

color

The colour spectrum used to display the heat map. The default is a "Spectral" diverging palette from the RColorBrewer package (see Details).

...

There are additional features available through this argument that can be used to customize the heatmap (see Details).

Details

This function is a rewrite of Bromans qtl package function plot.rf that provides extended functionality. When what = "lod" is chosen the pairwise LOD linkage between markers is displayed on the heat map with a legend on the right hand side spanning zero to lmax across the color spectrum. If what = "rf" the pairwise estimated recombination fractions are displayed on the heat map with a legend on the right hand side spanning rmin to 0.5 across the color spectrum. The legend also extends past 0.5 to display estimated recombination fractions between 0.5 and one through a colour spectrum of the maximum color value to white. This functionality now gives users the ability to detect markers that may be problematic or possibly out of phase. For what = "both" the pairwise LOD linkage is displayed on the lower triangle of the heat map and the pairwise estimated recombination fractions are displayed on the upper triangle. If this option is chosen, legends are displayed for both components of the heat map.

The default colour spectrum is the diverging palette "Spectral" from the RcolorBrewer package. This diverging palette provides an aesthetically pleasing colour spectrum for the diagnosis of pairwise linkage between markers. Specifically, the palette displays weak linkage and/or low recombination between markers as blue or "cool" areas and strong linkage and/or recombination between markers are shown as red or "hot" areas.

Much of the extra functionality of this function comes from the use of image.plot in the fields package. This function allows the partitioning of the plotting region into a bigplot region for the heat map and a smallplot region for the legend. This is called twice when what = "both". The size of the regions can be manipulated by passing the bigplot or smallplot arguments to the function but it is advised to use the defaults. Further manipulation of the heat map can achieved by passing other arguments of the function image.plot. Users should consult the help file for image.plot for more details. It should be noted that the argument legend.args needs to be avoided as it used in this function.

Value

A heat map is displayed on the current plotting device.

Author(s)

Julian Taylor

References

Taylor, J., Butler, D. (2017) R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis. Journal of Statistical Software, 79(6), 1–29.

See Also

plotRF

Examples

data(mapDH, package = "ASMap")

## bulking linkage groups and reconstructing entire linkage map

test1 <- mstmap(mapDH, bychr = FALSE, dist.fun = "kosambi",
                trace = FALSE)

## plot heat map of result

heatMap(test1, lmax = 30)