RangeTrack-class: RangeTrack class and methods
In Gviz: Plotting data and annotation information along genomic coordinates
Description
Objects from the class
Slots
Extends
Methods
Display Parameters
Author(s)
See Also
Examples
Description
The virtual parent class for all track items in the Gviz
package that contain some form of genomic ranges.
Objects from the class
A virtual class: No objects may be created from it.
Slots
range:Object of class GRanges,
the genomic ranges of the track items as well as additional
annotation information in its elementMetaData slot. Please
not that the slot is actually implemented as a class union between
GRanges and IRanges to increase
efficiency, for instance for DataTrack
objects. This usualy does not concern the user.
chromosome:Object of class "character", the
chromosome on which the track is defined. There can only be a
single chromosome for one track. For certain subclasses, the space
of allowed chromosome names is limited (e.g., only those
chromosomes that exist for a particular genome). Throughout the
package, chromosome name have to be entered either as a single
integer scalar or as a character scalar of the form
chrXYZ, where XYZ may be an arbitrary
character string.
genome:Object of class "character", the genome
for which the track is defined. For most sub-classes this has to
be valid UCSC genome identifier, however this may not always be
formally checked upon object instantiation.
dp:Object of class
DisplayPars, inherited from class
GdObject.
name:Object of class "character", inherited
from class GdObject
imageMap:Object of class
ImageMap, inherited from class
GdObject
Extends
Class "GdObject", directly.
Methods
In the following code chunks, obj is considered to be an object
of class RangeTrack.
Exported in the name space:
- [
signature(x="RangeTrack", i="ANY", j="ANY",
drop="ANY"): subset the items in the RangeTrack
object. This is essentially similar to subsetting of the
GRanges object in the range
slot. For most applications, the subset method may be
more appropriate.
Additional Arguments:
i, j: subsetting indices, j is
ignored.
drop: argument is ignored.
Examples:
obj[1:5]
- chromosome
signature(GdObject="RangeTrack"):
return the chromosome for which the track is defined.
Usage:
chromosome(GdObject)
Examples:
chromosome(obj)
- chromosome<-
signature(GdObject="RangeTrack"):
replace the value of the track's chromosome. This has to be a
valid UCSC chromosome identifier or an integer or character
scalar that can be reasonably coerced into one.
Usage:
chromosome<-(GdObject, value)
Additional Arguments:
value: replacement value.
Examples:
chromosome(obj) <- "chr12"
- start, end, width
signature(x="RangeTrack"): the
start or end coordinates of the track items, or their width in
genomic coordinates.
Usage:
start(x)
end(x)
width(x)
Examples:
start(obj)
end(obj)
width(obj)
- start<-, end<-, width<-
signature(x="RangeTrack"):
replace the start or end coordinates of the track items, or their
width.
Usage:
start<-(x, value)
end<-(x, value)
width<-(x, value)
Additional Arguments:
value: replacement value.
Examples:
start(obj) <- 1:10
end(obj) <- 20:30
width(obj) <- 1
- position
signature(GdObject="RangeTrack"): the
arithmetic mean of the track item's coordionates, i.e.,
(end(obj)-start(obj))/2.
Usage:
position(GdObject)
Examples:
position(obj)
- feature
signature(GdObject="RangeTrack"): return the
grouping information for track items. For certain sub-classes,
groups may be indicated by different color schemes when
plotting. See grouping or
AnnotationTrack and
GeneRegionTrack for details.
Usage:
feature(GdObject)
Examples:
feature(obj)
- feature<-
signature(gdObject="RangeTrack",
value="character"): set the grouping information for track
items. This has to be a factor vector (or another type of vector
that can be coerced into one) of the same length as the number of
items in the RangeTrack. See grouping or
AnnotationTrack and
GeneRegionTrack for details.
Usage:
feature<-(GdObject, value)
Additional Arguments:
value: replacement value.
Examples:
feature(obj) <- c("a", "a", "b", "c", "a")
- genome
signature(x="RangeTrack"): return the track's genome.
Usage:
genome(x)
Examples:
genome(obj)
- genome<-
signature(x="RangeTrack"): set the track's
genome. Usually this has to be a valid UCSC identifier, however
this is not formally enforced here.
Usage:
genome<-(x, value)
Additional Arguments:
value: replacement value.
Examples:
genome(obj) <- "mm9"
- length
signature(x="RangeTrack"): return the number
of items in the track.
Usage:
length(x)
Examples:
length(obj)
- range
signature(x="RangeTrack"): return the genomic
coordinates for the track as an object of class
IRanges.
Usage:
range(x)
Examples:
range(obj)
- ranges
signature(x="RangeTrack"): return the genomic
coordinates for the track along with all additional annotation
information as an object of class GRanges.
Usage:
ranges(x)
Examples:
ranges(obj)
- split
signature(x="RangeTrack"): split a
RangeTrack object by an appropriate factor vector (or
another vector that can be coerced into one). The output of this
operation is a list of objects of the same class as the input
object, all inheriting from class RangeTrack.
Usage:
split(x, f, ...)
Additional Arguments:
f: the splitting factor.
...: all further arguments are ignored.
Examples:
split(obj, c("a", "a", "b", "c", "a"))
- strand
signature(x="RangeTrack"): return a vector of
strand specifiers for all track items, in the form '+' for the
Watson strand, '-' for the Crick strand or '*' for either of the
two.
Usage:
strand(x)
Examples:
strand(obj)
- strand<-
signature(x="RangeTrack"): replace the
strand information for the track items. The replacement value
needs to be an appropriate scalar or vector of strand values.
Usage:
strand<-(x, value)
Additional Arguments:
value: replacement value.
Examples:
strand(obj) <- "+"
- values
signature(x="RangeTrack"): return all
additional annotation information except for the genomic coordinates
for the track items as a data.frame.
Usage:
values(x)
Examples:
values(obj)
- min
signature(...="RangeTrack"):
return the start position for the leftmost range item.
Examples:
min(obj)
- max
signature(...="RangeTrack"):
return the end position for the rightmost range item.
Examples:
max(obj)
- coerce
signature(from="RangeTrack", to="data.frame"):
coerce the GRanges object in the
range slot into a regular data.frame.
Examples:
as(obj, "data.frame")
- subset
signature(x="RangeTrack"): subset a
RangeTrack by coordinates and sort if necessary.
Usage:
subset(x, from, to, sort=FALSE, ...)
Additional Arguments:
from, to: the coordinates range to subset
to.
sort: sort the object after subsetting. Usually
not necessary.
...: additional arguments are ignored.
Examples:
subset(obj, from=10, to=20, sort=TRUE)
Internal methods:
- initialize
signature(.Object="RangeTrack"):
initialize the object.
Inherited methods:
- displayPars
signature(x="RangeTrack",
name="character"): list the value of the display parameter
name. See settings for details on display
parameters and customization.
Usage:
displayPars(x, name)
Examples:
displayPars(obj, "col")
- displayPars
signature(x="RangeTrack", name="missing"):
list the value of all available display parameters. See
settings for details on display parameters and
customization.
Examples:
displayPars(obj)
- getPar
signature(x="RangeTrack", name="character"):
alias for the displayPars method. See
settings for details on display parameters and
customization.
Usage:
getPar(x, name)
Examples:
getPar(obj, "col")
- getPar
signature(x="RangeTrack", name="missing"):
alias for the displayPars method. See
settings for details on display parameters and
customization.
Examples:
getPar(obj)
- displayPars<-
signature(x="RangeTrack", value="list"):
set display parameters using the values of the named list in
value. See settings for details on display
parameters and customization.
Usage:
displayPars<-(x, value)
Examples:
displayPars(obj) <- list(col="red", lwd=2)
- setPar
signature(x="RangeTrack", value="character"):
set the single display parameter name to value. Note
that display parameters in the RangeTrack class are
pass-by-reference, so no re-assignmnet to the symbol obj is
necessary. See settings for details on display
parameters and customization.
Usage:
setPar(x, name, value)
Additional Arguments:
name: the name of the display parameter to set.
Examples:
setPar(obj, "col", "red")
- setPar
signature(x="RangeTrack", value="list"): set
display parameters by the values of the named list in
value. Note that display parameters in the
RangeTrack class are pass-by-reference, so no re-assignmnet
to the symbol obj is necessary. See settings
for details on display parameters and customization.
Examples:
setPar(obj, list(col="red", lwd=2))
- group
signature(GdObject="RangeTrack"): return
grouping information for the individual items in the track. Unless
overwritten in one of the sub-classes, this usualy returns
NULL.
Usage:
group(GdObject)
Examples:
group(obj)
- names
signature(x="RangeTrack"): return the value of
the name slot.
Usage:
names(x)
Examples:
names(obj)
- names<-
signature(x="RangeTrack", value="character"):
set the value of the name slot.
Usage:
names<-(x, value)
Examples:
names(obj) <- "foo"
- coords
signature(ImageMap="RangeTrack"): return the
coordinates from the internal image map.
Usage:
coords(ImageMap)
Examples:
coords(obj)
- tags
signature(x="RangeTrack"): return the tags from the
internal image map.
Usage:
tags(x)
Examples:
tags(obj)
- drawAxis
signature(GdObject="RangeTrack"): add a
y-axis to the title panel of a track if necessary. Unless
overwritten in one of the sub-classes this usualy does not plot
anything and returns NULL.
Usage:
drawAxis(x, ...)
Additional Arguments:
...: all further arguments are ignored.
Examples:
Gviz:::drawAxis(obj)
- drawGrid
signature(GdObject="RangeTrack"): superpose a
grid on top of a track if necessary. Unless overwritten in one of
the sub-classes this usualy does not plot anything and returns
NULL.
Usage:
drawGrid(GdObject, ...)
Additional Arguments:
...: additional arguments are ignored.
Examples:
Gviz:::drawGrid(obj)
Display Parameters
No formal display parameters are defined for objects of class
RangeTrack.
Additional display parameters are being inherited from the respective
parent classes. Note that not all of them may have an effect on the
plotting of RangeTrack objects.
GdObject:
alpha=1: Numeric scalar. The transparency for
all track items.
alpha.title=NULL: Numeric scalar. The transparency
for the title panel.
background.legend="transparent": Integer or
character scalar. The background color for the legend.
background.panel="transparent": Integer or
character scalar. The background color of the content panel.
background.title="lightgray": Integer or character
scalar. The background color for the title panel.
cex=1: Numeric scalar. The overall font expansion
factor for all text and glyphs, unless a more specific
definition exists.
cex.axis=NULL: Numeric scalar. The expansion
factor for the axis annotation. Defaults to NULL, in
which case it is automatically determined based on the
available space.
cex.title=NULL: Numeric scalar. The expansion
factor for the title panel. This effects the fontsize of both
the title and the axis, if any. Defaults to NULL,
which means that the text size is automatically adjusted to
the available space.
col="#0080FF": Integer or character scalar.
Default line color setting for all plotting elements, unless
there is a more specific control defined elsewhere.
col.axis="white": Integer or character scalar.
The font and line color for the y axis, if any.
col.border.title="white": Integer or character
scalar. The border color for the title panels.
col.frame="lightgray": Integer or character
scalar. The line color used for the panel frame, if
frame==TRUE
col.grid="#808080": Integer or character scalar.
Default line color for grid lines, both when type=="g"
in DataTracks and when display parameter
grid==TRUE.
col.line=NULL: Integer or character scalar.
Default colors for plot lines. Usually the same as the global
col parameter.
col.symbol=NULL: Integer or character scalar.
Default colors for plot symbols. Usually the same as the
global col parameter.
col.title="white" (Aliases: fontcolor.title):
Integer or character scalar. The border color for the title panels
collapse=TRUE: Boolean controlling whether to
collapse the content of the track to accomodate the minimum
current device resolution. See collapsing for
details.
fill="lightgray": Integer or character scalar.
Default fill color setting for all plotting elements, unless
there is a more specific control defined elsewhere.
fontcolor="black": Integer or character scalar.
The font color for all text, unless a more specific definition
exists.
fontface=1: Integer or character scalar. The
font face for all text, unless a more specific definition exists.
fontface.title=2: Integer or character scalar.
The font face for the title panels.
fontfamily="sans": Integer or character scalar.
The font family for all text, unless a more specific definition
exists.
fontfamily.title="sans": Integer or character
scalar. The font family for the title panels.
fontsize=12: Numeric scalar. The font size for
all text, unless a more specific definition exists.
frame=FALSE: Boolean. Draw a frame around the
track when plotting.
grid=FALSE: Boolean, switching on/off the plotting
of a grid.
h=-1: Integer scalar. Parameter controlling the
number of horizontal grid lines, see panel.grid
for details.
lineheight=1: Numeric scalar. The font line
height for all text, unless a more specific definition exists.
lty="solid": Numeric scalar. Default line type
setting for all plotting elements, unless there is a more
specific control defined elsewhere.
lty.grid="solid": Integer or character scalar.
Default line type for grid lines, both when type=="g"
in DataTracks and when display parameter
grid==TRUE.
lwd=1: Numeric scalar. Default line width setting
for all plotting elements, unless there is a more specific
control defined elsewhere.
lwd.border.title=1: Integer scalar. The border
width for the title panels.
lwd.grid=1: Numeric scalar. Default line width
for grid lines, both when type=="g" in DataTracks
and when display parameter grid==TRUE.
lwd.title=1: Integer scalar. The border width
for the title panels
min.distance=1: Numeric scalar. The minimum
pixel distance before collapsing range items, only if
collapse==TRUE. See collapsing for details.
min.height=3: Numeric scalar. The minimum range
height in pixels to display. All ranges are expanded to this
size in order to avoid rendering issues. See collapsing
for details.
min.width=1: Numeric scalar. The minimum range
width in pixels to display. All ranges are expanded to this
size in order to avoid rendering issues. See collapsing
for details.
reverseStrand=FALSE: Logical scalar. Set up the
plotting coordinates in 3' -> 5' direction if TRUE.
This will effectively mirror the plot on the vertical axis.
rotation=0: The rotation angle for all text
unless a more specific definiton exists.
rotation.title=90 (Aliases: rotation.title):
The rotation angle for the text in the title panel. Even
though this can be adjusted, the automatic resizing of the
title panel will currently not work, so use at own risk.
showAxis=TRUE: Boolean controlling whether to
plot a y axis (only applies to track types where axes are
implemented).
showTitle=TRUE: Boolean controlling whether to
plot a title panel. Although this can be set individually
for each track, in multi-track plots as created by
plotTracks there will still be an empty
placeholder in case any of the other tracks include a title.
The same holds true for axes. Note that the the title panel
background color could be set to transparent in order to
completely hide it.
size=1: Numeric scalar. The relative size of
the track. Can be overridden in the plotTracks
function.
v=-1: Integer scalar. Parameter controlling the
number of vertical grid lines, see panel.grid
for details.
Author(s)
Florian Hahne
See Also
Examples
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## This is a refernce class therefore we show below
## an example from AnnotationTrack
## An empty object
AnnotationTrack()
## Construct from individual arguments
st <- c(2000000, 2070000, 2100000, 2160000)
ed <- c(2050000, 2130000, 2150000, 2170000)
str <- c("-", "+", "-", "-")
gr <- c("Group1","Group2","Group1", "Group3")
annTrack <- AnnotationTrack(start=st, end=ed, strand=str, chromosome=7,
genome="hg19", feature="test", group=gr,
id=paste("annTrack item", 1:4),
name="generic annotation", stacking="squish")
## Plotting
plotTracks(annTrack)
Gviz documentation built on March 16, 2021, 6:01 p.m.
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Description Objects from the class Slots Extends Methods Display Parameters Author(s) See Also Examples
Description
The virtual parent class for all track items in the Gviz package that contain some form of genomic ranges.
Objects from the class
A virtual class: No objects may be created from it.
Slots
range:Object of class
GRanges, the genomic ranges of the track items as well as additional annotation information in itselementMetaDataslot. Please not that the slot is actually implemented as a class union betweenGRangesandIRangesto increase efficiency, for instance forDataTrackobjects. This usualy does not concern the user.chromosome:Object of class
"character", the chromosome on which the track is defined. There can only be a single chromosome for one track. For certain subclasses, the space of allowed chromosome names is limited (e.g., only those chromosomes that exist for a particular genome). Throughout the package, chromosome name have to be entered either as a single integer scalar or as a character scalar of the formchrXYZ, where XYZ may be an arbitrary character string.genome:Object of class
"character", the genome for which the track is defined. For most sub-classes this has to be valid UCSC genome identifier, however this may not always be formally checked upon object instantiation.dp:Object of class
DisplayPars, inherited from classGdObject.name:Object of class
"character", inherited from classGdObjectimageMap:Object of class
ImageMap, inherited from classGdObject
Extends
Class "GdObject", directly.
Methods
In the following code chunks, obj is considered to be an object
of class RangeTrack.
Exported in the name space:
- [
signature(x="RangeTrack", i="ANY", j="ANY", drop="ANY"): subset the items in theRangeTrackobject. This is essentially similar to subsetting of theGRangesobject in therangeslot. For most applications, thesubsetmethod may be more appropriate.Additional Arguments:
i,j: subsetting indices,jis ignored.drop: argument is ignored.
Examples:
obj[1:5]
- chromosome
signature(GdObject="RangeTrack"): return the chromosome for which the track is defined.Usage:
chromosome(GdObject)Examples:
chromosome(obj)
- chromosome<-
signature(GdObject="RangeTrack"): replace the value of the track's chromosome. This has to be a valid UCSC chromosome identifier or an integer or character scalar that can be reasonably coerced into one.Usage:
chromosome<-(GdObject, value)Additional Arguments:
value: replacement value.
Examples:
chromosome(obj) <- "chr12"
- start, end, width
signature(x="RangeTrack"): the start or end coordinates of the track items, or their width in genomic coordinates.Usage:
start(x)end(x)width(x)Examples:
start(obj)end(obj)width(obj)
- start<-, end<-, width<-
signature(x="RangeTrack"): replace the start or end coordinates of the track items, or their width.Usage:
start<-(x, value)end<-(x, value)width<-(x, value)Additional Arguments:
value: replacement value.
Examples:
start(obj) <- 1:10end(obj) <- 20:30width(obj) <- 1
- position
signature(GdObject="RangeTrack"): the arithmetic mean of the track item's coordionates, i.e.,(end(obj)-start(obj))/2.Usage:
position(GdObject)Examples:
position(obj)
- feature
signature(GdObject="RangeTrack"): return the grouping information for track items. For certain sub-classes, groups may be indicated by different color schemes when plotting. SeegroupingorAnnotationTrackandGeneRegionTrackfor details.Usage:
feature(GdObject)Examples:
feature(obj)
- feature<-
signature(gdObject="RangeTrack", value="character"): set the grouping information for track items. This has to be a factor vector (or another type of vector that can be coerced into one) of the same length as the number of items in theRangeTrack. SeegroupingorAnnotationTrackandGeneRegionTrackfor details.Usage:
feature<-(GdObject, value)Additional Arguments:
value: replacement value.
Examples:
feature(obj) <- c("a", "a", "b", "c", "a")
- genome
signature(x="RangeTrack"): return the track's genome.Usage:
genome(x)Examples:
genome(obj)
- genome<-
signature(x="RangeTrack"): set the track's genome. Usually this has to be a valid UCSC identifier, however this is not formally enforced here.Usage:
genome<-(x, value)Additional Arguments:
value: replacement value.
Examples:
genome(obj) <- "mm9"
- length
signature(x="RangeTrack"): return the number of items in the track.Usage:
length(x)Examples:
length(obj)
- range
signature(x="RangeTrack"): return the genomic coordinates for the track as an object of classIRanges.Usage:
range(x)Examples:
range(obj)
- ranges
signature(x="RangeTrack"): return the genomic coordinates for the track along with all additional annotation information as an object of classGRanges.Usage:
ranges(x)Examples:
ranges(obj)
- split
signature(x="RangeTrack"): split aRangeTrackobject by an appropriate factor vector (or another vector that can be coerced into one). The output of this operation is a list of objects of the same class as the input object, all inheriting from classRangeTrack.Usage:
split(x, f, ...)Additional Arguments:
f: the splitting factor....: all further arguments are ignored.
Examples:
split(obj, c("a", "a", "b", "c", "a"))
- strand
signature(x="RangeTrack"): return a vector of strand specifiers for all track items, in the form '+' for the Watson strand, '-' for the Crick strand or '*' for either of the two.Usage:
strand(x)Examples:
strand(obj)
- strand<-
signature(x="RangeTrack"): replace the strand information for the track items. The replacement value needs to be an appropriate scalar or vector of strand values.Usage:
strand<-(x, value)Additional Arguments:
value: replacement value.
Examples:
strand(obj) <- "+"
- values
signature(x="RangeTrack"): return all additional annotation information except for the genomic coordinates for the track items as a data.frame.Usage:
values(x)Examples:
values(obj)
- min
signature(...="RangeTrack"): return the start position for the leftmost range item.Examples:
min(obj)
- max
signature(...="RangeTrack"): return the end position for the rightmost range item.Examples:
max(obj)
- coerce
signature(from="RangeTrack", to="data.frame"): coerce theGRangesobject in therangeslot into a regular data.frame.Examples:
as(obj, "data.frame")
- subset
signature(x="RangeTrack"): subset aRangeTrackby coordinates and sort if necessary.Usage:
subset(x, from, to, sort=FALSE, ...)Additional Arguments:
from,to: the coordinates range to subset to.sort: sort the object after subsetting. Usually not necessary....: additional arguments are ignored.
Examples:
subset(obj, from=10, to=20, sort=TRUE)
Internal methods:
- initialize
signature(.Object="RangeTrack"): initialize the object.
Inherited methods:
- displayPars
signature(x="RangeTrack", name="character"): list the value of the display parametername. Seesettingsfor details on display parameters and customization.Usage:
displayPars(x, name)Examples:
displayPars(obj, "col")
- displayPars
signature(x="RangeTrack", name="missing"): list the value of all available display parameters. Seesettingsfor details on display parameters and customization.Examples:
displayPars(obj)
- getPar
signature(x="RangeTrack", name="character"): alias for thedisplayParsmethod. Seesettingsfor details on display parameters and customization.Usage:
getPar(x, name)Examples:
getPar(obj, "col")
- getPar
signature(x="RangeTrack", name="missing"): alias for thedisplayParsmethod. Seesettingsfor details on display parameters and customization.Examples:
getPar(obj)
- displayPars<-
signature(x="RangeTrack", value="list"): set display parameters using the values of the named list invalue. Seesettingsfor details on display parameters and customization.Usage:
displayPars<-(x, value)Examples:
displayPars(obj) <- list(col="red", lwd=2)
- setPar
signature(x="RangeTrack", value="character"): set the single display parameternametovalue. Note that display parameters in theRangeTrackclass are pass-by-reference, so no re-assignmnet to the symbolobjis necessary. Seesettingsfor details on display parameters and customization.Usage:
setPar(x, name, value)Additional Arguments:
name: the name of the display parameter to set.
Examples:
setPar(obj, "col", "red")
- setPar
signature(x="RangeTrack", value="list"): set display parameters by the values of the named list invalue. Note that display parameters in theRangeTrackclass are pass-by-reference, so no re-assignmnet to the symbolobjis necessary. Seesettingsfor details on display parameters and customization.Examples:
setPar(obj, list(col="red", lwd=2))
- group
signature(GdObject="RangeTrack"): return grouping information for the individual items in the track. Unless overwritten in one of the sub-classes, this usualy returnsNULL.Usage:
group(GdObject)Examples:
group(obj)
- names
signature(x="RangeTrack"): return the value of thenameslot.Usage:
names(x)Examples:
names(obj)
- names<-
signature(x="RangeTrack", value="character"): set the value of thenameslot.Usage:
names<-(x, value)Examples:
names(obj) <- "foo"
- coords
signature(ImageMap="RangeTrack"): return the coordinates from the internal image map.Usage:
coords(ImageMap)Examples:
coords(obj)
- tags
signature(x="RangeTrack"): return the tags from the internal image map.Usage:
tags(x)Examples:
tags(obj)
- drawAxis
signature(GdObject="RangeTrack"): add a y-axis to the title panel of a track if necessary. Unless overwritten in one of the sub-classes this usualy does not plot anything and returnsNULL.Usage:
drawAxis(x, ...)Additional Arguments:
...: all further arguments are ignored.
Examples:
Gviz:::drawAxis(obj)
- drawGrid
signature(GdObject="RangeTrack"): superpose a grid on top of a track if necessary. Unless overwritten in one of the sub-classes this usualy does not plot anything and returnsNULL.Usage:
drawGrid(GdObject, ...)Additional Arguments:
...: additional arguments are ignored.
Examples:
Gviz:::drawGrid(obj)
Display Parameters
No formal display parameters are defined for objects of class
RangeTrack.
Additional display parameters are being inherited from the respective
parent classes. Note that not all of them may have an effect on the
plotting of RangeTrack objects.
GdObject:alpha=1: Numeric scalar. The transparency for all track items.alpha.title=NULL: Numeric scalar. The transparency for the title panel.background.legend="transparent": Integer or character scalar. The background color for the legend.background.panel="transparent": Integer or character scalar. The background color of the content panel.background.title="lightgray": Integer or character scalar. The background color for the title panel.cex=1: Numeric scalar. The overall font expansion factor for all text and glyphs, unless a more specific definition exists.cex.axis=NULL: Numeric scalar. The expansion factor for the axis annotation. Defaults toNULL, in which case it is automatically determined based on the available space.cex.title=NULL: Numeric scalar. The expansion factor for the title panel. This effects the fontsize of both the title and the axis, if any. Defaults toNULL, which means that the text size is automatically adjusted to the available space.col="#0080FF": Integer or character scalar. Default line color setting for all plotting elements, unless there is a more specific control defined elsewhere.col.axis="white": Integer or character scalar. The font and line color for the y axis, if any.col.border.title="white": Integer or character scalar. The border color for the title panels.col.frame="lightgray": Integer or character scalar. The line color used for the panel frame, ifframe==TRUEcol.grid="#808080": Integer or character scalar. Default line color for grid lines, both whentype=="g"inDataTracks and when display parametergrid==TRUE.col.line=NULL: Integer or character scalar. Default colors for plot lines. Usually the same as the globalcolparameter.col.symbol=NULL: Integer or character scalar. Default colors for plot symbols. Usually the same as the globalcolparameter.col.title="white"(Aliases: fontcolor.title): Integer or character scalar. The border color for the title panelscollapse=TRUE: Boolean controlling whether to collapse the content of the track to accomodate the minimum current device resolution. Seecollapsingfor details.fill="lightgray": Integer or character scalar. Default fill color setting for all plotting elements, unless there is a more specific control defined elsewhere.fontcolor="black": Integer or character scalar. The font color for all text, unless a more specific definition exists.fontface=1: Integer or character scalar. The font face for all text, unless a more specific definition exists.fontface.title=2: Integer or character scalar. The font face for the title panels.fontfamily="sans": Integer or character scalar. The font family for all text, unless a more specific definition exists.fontfamily.title="sans": Integer or character scalar. The font family for the title panels.fontsize=12: Numeric scalar. The font size for all text, unless a more specific definition exists.frame=FALSE: Boolean. Draw a frame around the track when plotting.grid=FALSE: Boolean, switching on/off the plotting of a grid.h=-1: Integer scalar. Parameter controlling the number of horizontal grid lines, seepanel.gridfor details.lineheight=1: Numeric scalar. The font line height for all text, unless a more specific definition exists.lty="solid": Numeric scalar. Default line type setting for all plotting elements, unless there is a more specific control defined elsewhere.lty.grid="solid": Integer or character scalar. Default line type for grid lines, both whentype=="g"inDataTracks and when display parametergrid==TRUE.lwd=1: Numeric scalar. Default line width setting for all plotting elements, unless there is a more specific control defined elsewhere.lwd.border.title=1: Integer scalar. The border width for the title panels.lwd.grid=1: Numeric scalar. Default line width for grid lines, both whentype=="g"inDataTracks and when display parametergrid==TRUE.lwd.title=1: Integer scalar. The border width for the title panelsmin.distance=1: Numeric scalar. The minimum pixel distance before collapsing range items, only ifcollapse==TRUE. Seecollapsingfor details.min.height=3: Numeric scalar. The minimum range height in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. Seecollapsingfor details.min.width=1: Numeric scalar. The minimum range width in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. Seecollapsingfor details.reverseStrand=FALSE: Logical scalar. Set up the plotting coordinates in 3' -> 5' direction ifTRUE. This will effectively mirror the plot on the vertical axis.rotation=0: The rotation angle for all text unless a more specific definiton exists.rotation.title=90(Aliases: rotation.title): The rotation angle for the text in the title panel. Even though this can be adjusted, the automatic resizing of the title panel will currently not work, so use at own risk.showAxis=TRUE: Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).showTitle=TRUE: Boolean controlling whether to plot a title panel. Although this can be set individually for each track, in multi-track plots as created byplotTracksthere will still be an empty placeholder in case any of the other tracks include a title. The same holds true for axes. Note that the the title panel background color could be set to transparent in order to completely hide it.size=1: Numeric scalar. The relative size of the track. Can be overridden in theplotTracksfunction.v=-1: Integer scalar. Parameter controlling the number of vertical grid lines, seepanel.gridfor details.
Author(s)
Florian Hahne
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ## This is a refernce class therefore we show below
## an example from AnnotationTrack
## An empty object
AnnotationTrack()
## Construct from individual arguments
st <- c(2000000, 2070000, 2100000, 2160000)
ed <- c(2050000, 2130000, 2150000, 2170000)
str <- c("-", "+", "-", "-")
gr <- c("Group1","Group2","Group1", "Group3")
annTrack <- AnnotationTrack(start=st, end=ed, strand=str, chromosome=7,
genome="hg19", feature="test", group=gr,
id=paste("annTrack item", 1:4),
name="generic annotation", stacking="squish")
## Plotting
plotTracks(annTrack)
|
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