plot.bim.loci {bim} | R Documentation |
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, yandell@stat.wisc.edu
http://www.stat.wisc.edu/~yandell/qtl/software/Bmapqtl
data( vern ) data( verngeo.bim ) plot.bim.loci( verngeo.bim, vern, 2 )