"trackViewerStyle"trackViewerStyle-class.RdAn object of class "trackViewerStyle"
represents track viewer style.
trackViewerStyle(...)
setTrackViewerStyleParam(tvs, attr, value)
# S4 method for class 'trackViewerStyle,character'
setTrackViewerStyleParam(tvs, attr, value)An object of class trackViewerStyle with the modified
slot, returned invisibly. The variable supplied as tvs is updated as
a side effect.
setTrackViewerStyleParam changes one slot of a
trackViewerStyle object. Unlike setTrackStyleParam and
its siblings, this style is not attached to a single track: it controls the
figure-wide x-axis shared by every track in a plot (drawn once, beneath the
bottom-most track), so this function is typically called on the
trackViewerStyle object passed to viewTracks, not on a track
itself.
Accepted values of attr, all slots of trackViewerStyle:
margin"numeric" of length 4, the bottom, left, top
and right margins of the whole plot, as fractions of the device (each
value must be between 0 and 0.8). Default c(.01, .05, 0, 0).
xlas"numeric" in {0, 1, 2, 3}, the rotation of the
x-axis tick labels. See par:las. Ignored when
autolas is TRUE.
xgp"list" of graphical parameters for the x-axis,
converted to gpar, e.g. list(cex=.8, col="black").
For the equivalent y-axis settings, see yaxisStyle and
setTrackYaxisParam, which are per-track rather than
figure-wide.
xaxis"logical", whether the shared x-axis is drawn at
all. Default FALSE.
xat"numeric" vector of genomic positions at which
x-axis tick marks are drawn, passed to grid.xaxis as at. If
left at its default (numeric(0)), positions are chosen
automatically from the plotted range.
xlabel"character" vector of labels for the ticks in
xat, passed to grid.xaxis as label. Should be the
same length as xat when both are set explicitly; left at its
default, labels are generated automatically from the tick positions.
autolas"logical", whether the y-axis label direction
is chosen automatically rather than following xlas. Default
FALSE.
flip"logical", whether the x-axis (and the whole
plot) is flipped, e.g. to display a feature on the minus strand
5' to 3' left to right. Default FALSE.
Any other value of attr is rejected. Values are assigned with
check = TRUE, so the validity method of
trackViewerStyle runs on every call — an xlas outside
0:3 or a margin outside [0, 0.8] fails immediately with a descriptive
message rather than surfacing later as a plotting error.
margin"numeric", specify the bottom, left, top and right margin.
xlas"numeric", label direction of x-axis mark. It should
be a integer 0-3. See par:las
xgpA "list", object, It will convert to an object of
class gpar. This is basically a list of graphical
parameter settings of x-axis. For y-axis, see yaxisStyle
xaxis"logical", draw x-axis or not
xat"numeric", the values will be passed to grid.xaxis as
'at' parameter.
xlabel"character", the values will be passed to grid.xaxis as
'label' parameter.
autolas"logical" automatic determine y label direction
flip"logical" flip the x-axis or not, default FALSE
Like setTrackStyleParam, this method assigns the updated
object back to the variable passed as tvs in the caller's
environment, so setTrackViewerStyleParam(tvs, "xaxis", TRUE) is
sufficient on its own and the result need not be re-assigned. It is also
returned invisibly for use in contexts, such as lapply, where that
calling-frame assignment has no visible target — see
setTrackStyleParam for a worked example of that case.
trackViewerStyle, setTrackStyleParam,
setTrackXscaleParam, setTrackYaxisParam
tvs <- trackViewerStyle()
setTrackViewerStyleParam(tvs, "xaxis", TRUE)
tvs <- trackViewerStyle()
## turn on the shared x-axis and rotate its labels
setTrackViewerStyleParam(tvs, "xaxis", TRUE)
setTrackViewerStyleParam(tvs, "xlas", 2)
## choose explicit tick positions and labels
setTrackViewerStyleParam(tvs, "xat", c(122929000, 122929500, 122930000))
setTrackViewerStyleParam(tvs, "xlabel", c("122,929,000", "122,929,500", "122,930,000"))
## tighten the plot margins
setTrackViewerStyleParam(tvs, "margin", c(.02, .08, .01, .01))
## flip the plot, e.g. for a minus-strand gene
setTrackViewerStyleParam(tvs, "flip", TRUE)
if (FALSE) { # \dontrun{
## rejected: xlas must be one of 0:3
setTrackViewerStyleParam(tvs, "xlas", 5)
## rejected: not a slot of trackViewerStyle
setTrackViewerStyleParam(tvs, "color", "red")
} # }