plotFamilyLods: Plot family contribution to peak LOD

Description

Plot the top N families that contribute to the peak LOD score as obtained from a multic object

Usage

plotFamilyLods(x, npeakfams=5, title=NULL, title.cex=0.75, legend=T,
               legend.loc=c("left", "middle", "right", "extra"),
               type=c("top", "total", "proportion", "all"), ...)

Arguments

a multic object

npeakfams

number of top families to plot

title

title for the plot

title.cex

character size for the title

legend

logical (default = TRUE) indicating whether a legend is displayed or not

legend.loc

character string indicating the general legend location, if legend =T. "left" indicates the top left, "right" indicates the top right, "middle" indicates the upper middle, and "extra" indicates the legend should go on a separate plot.

type

character string indicating which plot should be shown. "top" shows the top npeakfams families, "total" shows the top families plus the overall total, "proportion" shows the percentage for the top families of the total LOD score, and "all" shows all 3 pl

...

additional parameters to alter the default behavior of the plot.

Value

the lod scores for the top families

Details

Based on the peak total lod score for the multic object, determine which families contribute most to that peak. Then display their contribution across the entire area that was used to fit the multic object.

Examples

Run this code

mult10 <- multic(sys.avg ~ sex + agexam + agexam^2, data=d10,
                 famid=famid, id=id, dadid=fa, momid=mo, sex=sex,
                 mloci='multicInput/mloci.out.gz', share='multicInput/share.out.gz',
                 calc.fam.log.liks=T)

plotFamilyLods(mult10, npeakfams=3, plot="total")