GdObject-class: GdObject class and methods
In Gviz: Plotting data and annotation information along genomic coordinates
Description
Objects from the class
Slots
Methods
Display Parameters
Author(s)
See Also
Examples
Description
The virtual parent class for all track items in the Gviz
package. This class definition contains all the common entities that
are needed for a track to be plotted. During object instantiation for
any of the sub-classes inheriting from GdObject, this class'
global ininitializer has to be called in order to assure that all
necessary settings are present.
Objects from the class
A virtual class: No objects may be created from it.
Slots
dp:Object of class
DisplayPars, the display settings
controlling the look and feel of a track. See
settings for details on setting graphical parameters
for tracks.
name:Object of class "character", a
human-readable name for the track that will be used in the track's
annotation panel if necessary.
imageMap:Object of class
ImageMap, containing optional information
for an HTML image map. This will be created by the drawGD
methods when the track is plotted to a device and is usually not set
by the user.
Methods
In the following code chunks, obj is considered to be an object
of class GdObject.
Exported in the name space:
- displayPars
signature(x="GdObject", 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="GdObject", 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="GdObject", 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="GdObject", name="missing"): alias
for the displayPars method. See settings for
details on display parameters and customization.
Examples:
getPar(obj)
- displayPars<-
signature(x="GdObject", 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="GdObject", value="character"): set
the single display parameter name to value. Note
that display parameters in the GdObject 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="GdObject", value="list"): set
display parameters by the values of the named list in
value. Note that display parameters in the GdObject
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="GdObject"): 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="GdObject"): return the value of
the name slot.
Usage:
names(x)
Examples:
names(obj)
- names<-
signature(x="GdObject", value="character"):
set the value of the name slot.
Usage:
names<-(x, value)
Examples:
names(obj) <- "foo"
- coords
signature(ImageMap="GdObject"): return the
coordinates from the internal image map.
Usage:
coords(ImageMap)
Examples:
coords(obj)
- tags
signature(x="GdObject"): return the tags from the
internal image map.
Usage:
tags(x)
Examples:
tags(obj)
- subset
signature(x="GdObject"): subset a
GdObject by coordinates. Most of the respective sub-classes
inheriting from GdObject overwrite this method, the default
is to return the unaltered input object.
Usage:
subset(x, ...)
Additional Arguments:
...: all further arguments are ignored.
Examples:
subset(obj)
Internal methods:
- drawAxis
signature(GdObject="GdObject"): 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="GdObject"): 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)
- initialize
signature(.Object="GdObject"): initialize
the object. This involves setting up a new environment for the
display parameters and filling it up with the current
settings. All arguments that have not been clobbered up by one of
the sub-class initializers are considered to be additional display
parameters and are also added to the environment. See
settings for details on setting graphical parameters
for tracks.
Display Parameters
The following display parameters are set for objects of class
GdObject upon instantiation, unless one or more of them have
already been set by one of the optional sub-class initializers, which
always get precedence over these global defaults. See settings
for details on setting graphical parameters for tracks.
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.
...: additional display parameters are allowed.
Those typically take the value of a valid R color descriptors.
The parameter names will later be matched to optional track item
types as defined in the 'feature' range attribute, and all tracks
of the matched types are colored accordingly. See the documentation
of the GeneRegionTrack and AnnotationTrack
classes as well as grouping 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 Methods Display Parameters Author(s) See Also Examples
Description
The virtual parent class for all track items in the Gviz
package. This class definition contains all the common entities that
are needed for a track to be plotted. During object instantiation for
any of the sub-classes inheriting from GdObject, this class'
global ininitializer has to be called in order to assure that all
necessary settings are present.
Objects from the class
A virtual class: No objects may be created from it.
Slots
dp:Object of class
DisplayPars, the display settings controlling the look and feel of a track. Seesettingsfor details on setting graphical parameters for tracks.name:Object of class
"character", a human-readable name for the track that will be used in the track's annotation panel if necessary.imageMap:Object of class
ImageMap, containing optional information for an HTML image map. This will be created by thedrawGDmethods when the track is plotted to a device and is usually not set by the user.
Methods
In the following code chunks, obj is considered to be an object
of class GdObject.
Exported in the name space:
- displayPars
signature(x="GdObject", 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="GdObject", name="missing"): list the value of all available display parameters. Seesettingsfor details on display parameters and customization.Examples:
displayPars(obj)
- getPar
signature(x="GdObject", name="character"): alias for thedisplayParsmethod. Seesettingsfor details on display parameters and customization.Usage:
getPar(x, name)Examples:
getPar(obj, "col")
- getPar
signature(x="GdObject", name="missing"): alias for thedisplayParsmethod. Seesettingsfor details on display parameters and customization.Examples:
getPar(obj)
- displayPars<-
signature(x="GdObject", 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="GdObject", value="character"): set the single display parameternametovalue. Note that display parameters in theGdObjectclass 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="GdObject", value="list"): set display parameters by the values of the named list invalue. Note that display parameters in theGdObjectclass 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="GdObject"): 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="GdObject"): return the value of thenameslot.Usage:
names(x)Examples:
names(obj)
- names<-
signature(x="GdObject", value="character"): set the value of thenameslot.Usage:
names<-(x, value)Examples:
names(obj) <- "foo"
- coords
signature(ImageMap="GdObject"): return the coordinates from the internal image map.Usage:
coords(ImageMap)Examples:
coords(obj)
- tags
signature(x="GdObject"): return the tags from the internal image map.Usage:
tags(x)Examples:
tags(obj)
- subset
signature(x="GdObject"): subset aGdObjectby coordinates. Most of the respective sub-classes inheriting fromGdObjectoverwrite this method, the default is to return the unaltered input object.Usage:
subset(x, ...)Additional Arguments:
...: all further arguments are ignored.
Examples:
subset(obj)
Internal methods:
- drawAxis
signature(GdObject="GdObject"): 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="GdObject"): 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)
- initialize
signature(.Object="GdObject"): initialize the object. This involves setting up a new environment for the display parameters and filling it up with the current settings. All arguments that have not been clobbered up by one of the sub-class initializers are considered to be additional display parameters and are also added to the environment. Seesettingsfor details on setting graphical parameters for tracks.
Display Parameters
The following display parameters are set for objects of class
GdObject upon instantiation, unless one or more of them have
already been set by one of the optional sub-class initializers, which
always get precedence over these global defaults. See settings
for details on setting graphical parameters for tracks.
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....: additional display parameters are allowed. Those typically take the value of a valid R color descriptors. The parameter names will later be matched to optional track item types as defined in the 'feature' range attribute, and all tracks of the matched types are colored accordingly. See the documentation of theGeneRegionTrackandAnnotationTrackclasses as well asgroupingfor 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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