plot.qb.scantwo {qtlbim} | R Documentation |
Plots joint LOD for chromosomes on a two dimensional grid.
print.qb.scantwo(x, ...) plot.qb.scantwo(x, chr, smooth = 0, main, offset, lower = "joint", nodiag, slice = NULL, show.locus = TRUE, verbose = FALSE, ...)
x |
An object of class qb.scantwo . |
chr |
Vector of chromosomes to plot. Must be integer. |
smooth |
Perform smoothing of smooth nearest neighbors. |
main |
Main title. |
offset |
Offset to make all values non-negative (see below). |
lower |
This parameter is passed on to the
plot.scanone function. |
nodiag |
If TRUE do not include diagonal in plot. |
slice |
Take 1-D slice through 2-D surface is not NULL
(see below). |
show.locus |
If a slice , show locus estimate if TRUE . |
verbose |
Give verbose feedback if TRUE . |
... |
Other parameters passed to generic plot function. |
The offset
is used only if \line{qb.scantwo}
used
type
= "estimate" to make values for plotting all
non-negative. Values are rescaled by offset
so that the origin is
at 1 and, by default, the min and max are at 0 and 2, respectively, for
each half of the plot. We need this at this time because
plot.scantwo
does not allow negative values.
The plot.scantwo
arguments lower
and nodiag
are set to ensure values are all shown and not modified by
plot.scantwo
. The user is free to change them, but the
plots may be non-sensical. For instance, change to lower =
"cond-int"
produces much white area on the image.
A non-null slice
yields a 1-D view of the 2-D surface. The plots
for slices use plot.scantwo
. The elements of the slice
vector are:
TRUE
.chr
(default = 0).chr
(default = end of
chromosome).chr
by number of MCMC
samples: 0 = unweigthed; 1 = uniform weighting; 2 = position-specific
weighting (default).The scantwo object being plotted.
Brian S. Yandell, yandell@stat.wisc.edu
example(qb.scantwo)