plot.bim.loci {bim}R Documentation

Jittered plot of Bayesian QTL loci samples by chromosome


Each point is one locus from the Bayesian QTL estimates, plotted vertically by chromosome, jittered to give a sense of density.


plot.bim.loci(x, cross, nqtl=1, pattern=NULL, exact=FALSE,
  chr, labels=TRUE, amount=.35, cex, ... )


x object of class bim
cross corresponding object of class cross (extracted by bim.cross if not provided)
nqtl subset on number of QTL
pattern subset on chromosome pattern of QTL
exact subset on exact pattern or number of QTL if true
chr subset of chromosomes to plot (numerical indices or chromosome names)
labels include marker labels if TRUE
amount amount of jitter (between 0 and .45)
cex character expansion (may be invisible if too small–default set by bim.cex)
... graphical parameters can be given as arguments to plot


Focuses attention on chromosome lengths and concentration of QTL loci estimates. Horizontal blue lines at markers if cross included. Adjust amount and cex to modify look of plot. Most useful when looking at multiple chromosomes.


Brian S. Yandell,


See Also



data( vern )
data( verngeo.bim )

plot.bim.loci( verngeo.bim, vern, 2 )

[Package bim version 1.01-1 Index]