grid.plot.Probes {splicegear} | R Documentation |
Plot objects defined in the package splicegear
grid.plot.Probes(x, col = "black", add = FALSE, probepos.yscale = NULL, xlim = NULL, vp = NULL, ...) grid.plot.SpliceSites(x, col.typeI = "orange", col.typeI.window = "yellow", col.typeII = "red", add = FALSE, ylim = NULL, vp = NULL, ...) grid.plot.SpliceExprSet(x, probes.opt = list(), expr.opt = list(col = NA, lty = 1:6), fig.xratio = c(2, 1), fig.yratio = c(2, 1), probepos.yscale = NULL, ylim = NULL, ...)
x |
object of Probes-class ,
SpliceSites-class or
SpliceExprSet-class |
add |
add to an existing plot |
col |
color(s) for the probes (recycled if necessary). |
col.typeI |
color(s) for the type I spliced out exons |
col.typeI.window |
background color for the type I spliced out `windows' |
col.typeII |
color for the type II splicing events |
expr.opt |
list of options to plot expression values |
probepos.yscale |
specify coordinates on the y-axis for the probes. |
probes.opt |
options to plot the probes |
fig.xratio |
ratio for the left and right parts of the plot |
fig.yratio |
ratio for the upper and lower parts of the plot |
vp |
a viewport (grid package stuff) |
xlim |
range for the x-axis (see plot ). |
ylim |
range for the y-axis |
... |
optional parameters |
The `type I'/'type II' thing is described in the references found in
the help files for plot.SpliceSites
.
These functions are mainly used for their side effects.
grid.plot.SpliceSites
returns the range for the y-axis when
needed.
plot.SpliceSites, plot.Probes
## plot splice sites data(spsites) grid.plot(spsites) ## plot probes data(probes) grid.plot(probes) ## combined plot grid.plot(probes, spsites)