AlignedReadTrack-class: DEPRECATED! AlignedReadTrack class and methods)
In Gviz: Plotting data and annotation information along genomic coordinates
Description
Usage
Arguments
Value
Objects from the Class
Slots
Extends
Methods
Display Parameters
Author(s)
See Also
Examples
Description
DEPRECATED! This class and methods are deprecated, please use DataTrack,
AnnotationTrack or AlignmentsTrack instead.
A class to represent short sequences that have been aligned to a
reference genome as they are typically generated in a next generation
sequencing experiment.
Usage
1
2
Arguments
range
An object of class GRanges, or a
data.frame which will be coerced into one in which case it
needs to contain at least the three columns:
start, end: the start and end coordinates
for the track items.
strand: the strand information for the track
items. It may be provided in the form + for the Watson
strand, - for the Crick strand or * for either one
of the two.
Alternatively, the range argument may be missing, in which
case the relevant information has to be provided as individual
function arguments (see below).
start, end, width
Integer vectors, giving the start and the end
end coordinates for the individual track items, or their width. Two
of the three need to be specified, and have to be of equal length or
of length one, in which case this value will be recycled. Otherwise,
the usual R recycling rules for vectors do not apply.
strand
Character vector, the strand information for the
individual track items. Needs to be of equal length as the
start, end or width vectors, or of length 1. Please
note that grouped items need to be on the same strand, and erroneous
entries will result in casting of an error.
chromosome
The chromosome on which the track's genomic ranges
are defined. A valid UCSC chromosome identifier. Please note that at
this stage only syntactic checking takes place, i.e., the argument
value needs to be a single integer, numeric character or a character
of the form chrx, where x may be any
possible string. The user has to make sure that the respective
chromosome is indeed defined for the the track's genome.
genome
The genome on which the track's ranges are
defined. Usually this is a valid UCSC genome identifier, however
this is not being formally checked at this point.
stacking
The stacking type for overlapping items of the
track. One in c(hide, dense, squish, pack,full). Currently,
only hide (don't show the track items, squish (make best use of the
available space) and dense (no stacking at all) are implemented.
name
Character scalar of the track's name used in the title
panel when plotting.
coverageOnly
Instead of storing individual reads, just compute
the coverage and store the resulting coverage vector.
...
Additional items which will all be interpreted as further
display parameters.
Value
The return value of the constructor function is a new object of class
AlignedReadTrack.
Objects from the Class
Objects can be created using the constructor function AlignedReadTrack.
Slots
coverage:Object of class "list", a list of
coverage vectors for the plus strand, the minus strand and for
both strands combined.
coverageOnly:Object of class "logical", flag
to determine whether the object stores read locations or the coverage
vectors only.
stacking:Object of class "character",
inherited from class StackedTrack
stacks:Object of class "environment",
inherited from class StackedTrack
range:Object of class GRanges,
inherited from class RangeTrack
chromosome:Object of class "character",
inherited from class RangeTrack
genome:Object of class "character", inherited
from class RangeTrack
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 "StackedTrack", directly.
Class "RangeTrack", by class "StackedTrack",
distance2.
Class "GdObject", by class "StackedTrack",
distance3.
Methods
In the following code chunks, obj is considered to be an object
of class AlignedReadTrack.
Exported in the name space:
- [
signature(x="AlignedReadTrack"): subset the items in
the AlignedReadTrack. This is essentially similar to
subsetting of the GRanges object in the
range slot. For most applications, the subset method
may be more appropriate. The operation is only supported for
objects that still contain all the read locations, i.e.,
coverageOnly=FALSE.
Additional Arguments:
i: subsetting indices
Examples:
obj[1:5]
- subset
signature(x="AlignedReadTrack"): subset a
AlignedReadTrack by coordinates and sort if necessary.
Usage:
subset(x, from, to, sort=FALSE, stacks=FALSE)
Additional Arguments:
from, to: the coordinates range to subset
to.
sort: sort the object after subsetting. Usually
not necessary.
stacks: recompute the stacking after subsetting
which can be expensive and is not always necessary.
Examples:
subset(obj, from=10, to=20)
subset(obj, from=10, to=20, sort=TRUE, stacks=FALSE)
- split
signature(x="AlignedReadTrack"): split an
AlignedReadTrack object by an appropriate factor vector (or
another vector that can be coerced into one). The output of this
operation is a list of AlignedReadTrack objects.
Additional Arguments:
f: the splitting factor.
...: all further arguments are ignored.
Usage:
split(x, f, ...)
Examples:
split(obj, c("a", "a", "b", "c", "a"))
- coverage
signature(x="AlignedReadTrack"): return the
coverage vector for one of the strands, or the combined vector.
Usage:
coverage(x, strand="*")
Additional Arguments:
strand: the selector for the strand, + for
the Watson strand, - for the Crick strand or *
for both strands.
Examples:
coveraget(obj)
coverage(obj, strand="-")
Internal methods:
- setCoverage
signature(GdObject="AlignedReadTrack"):
recompute the coverage on the plus and minus strand as well as for
the combined strands and update the respective slot.
Usage:
setCoverage(GdObject)
Examples:
setCoverage(obj)
- drawAxis
signature(GdObject="AlignedReadTrack"): add a y-axis
to the title panel of a track.
Usage:
drawAxis(GdObject, from, to, subset=FALSE, ...)
Additional Arguments:
from, to: compute axis range from the data
within a certain coordinates range only.
subset: subset the object prior to calculating
the axis ranges. Can be expensive and is not always needed.
...: all further arguments are ignored.
Examples:
Gviz:::drawAxis(obj)
- drawGD
signature(gdObject="AlignedReadTrack"): plot the
object to a graphics device. The return value of this method is
the input object, potentially updated during the plotting
operation. Internally, there are two modes in which the method can
be called. Either in 'prepare' mode, in which case no plotting is
done but the object is preprocessed based on the
available space, or in 'plotting' mode, in which case the actual
graphical output is created. Since subsetting of the object can be
potentially costly, this can be switched off in case subsetting
has already been performed before or is not necessary.
Usage:
drawGD(GdObject, minBase, maxBase, prepare=FALSE,
subset=TRUE, ...)
Additional Arguments:
minBase, maxBase: the coordinate range to
plot.
prepare: run method in preparation or in
production mode.
subset: subset the object to the visible region
or skip the potentially expensive subsetting operation.
...: all further arguments are ignored.
Examples:
Gviz:::drawGD(obj)
Gviz:::drawGD(obj, minBase=1, maxBase=100)
Gviz:::drawGD(obj, prepare=TRUE,
subset=FALSE)
- drawGrid
signature(GdObject="AlignedReadTrack"): superpose a grid on top of a track.
Usage:
drawGrid(GdObject, from, to)
Additional Arguments:
from, to: draw grid within a certain
coordinates range. This needs to be supplied for the plotting
function to know the current genomic coordinates.
Examples:
Gviz:::drawGrid(obj, from=10, to=100)
- initialize
signature(.Object="AligendReadTrack"):
initialize the object.
- show
signature(object="AlignedReadTrack"): show a
human-readable summary of the object.
Inherited methods:
- stacking
signature(GdObject="AlignedReadTrack"): return
the current stacking type.
Usage:
stacking(GdObject)
Examples:
stacking(obj)
- stacking<-
signature(GdObject="AlignedReadTrack",
value="character"): set the object's stacking type to one in
c(hide, dense, squish, pack,full).
Usage:
stacking<-(GdObject, value)
Additional Arguments:
value: replacement value.
Examples:
stacking(obj) <- "squish"
- setStacks
signature(GdObject="AlignedReadTrack"):
recompute the stacks based on the available space and on the
object's track items and stacking settings.
Usage:
setStacks(GdObject, from, to)
Additional Arguments:
from, to: compute stacking within a
certain coordinates range. This needs to be supplied for the
plotting function to know the current genomic coordinates.
Examples:
Gviz:::setStacks(obj)
- stacks
signature(GdObject="AlignedReadTrack"): return
the stack indices for each track item.
Usage:
stacks(GdObject)
Examples:
Gviz:::stacks(obj)
- chromosome
signature(GdObject="AlignedReadTrack"):
return the chromosome for which the track is defined.
Usage:
chromosome(GdObject)
Examples:
chromosome(obj)
- chromosome<-
signature(GdObject="AlignedReadTrack"):
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="AlignedReadTrack"): 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="AlignedReadTrack"):
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="AlignedReadTrack"): 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="AlignedReadTrack"): 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="AlignedReadTrack",
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 AlignedReadTrack. 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="AlignedReadTrack"): return the track's genome.
Usage:
genome(x)
Examples:
genome(obj)
- genome<-
signature(x="AlignedReadTrack"): 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="AlignedReadTrack"): return the number
of items in the track.
Usage:
length(x)
Examples:
length(obj)
- range
signature(x="AlignedReadTrack"): return the genomic
coordinates for the track as an object of class
IRanges.
Usage:
range(x)
Examples:
range(obj)
- ranges
signature(x="AlignedReadTrack"): 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)
- strand
signature(x="AlignedReadTrack"): 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="AlignedReadTrack"): 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="AlignedReadTrack"): return all
additional annotation information except for the genomic coordinates
for the track items as a data.frame.
Usage:
values(x)
Examples:
values(obj)
- coerce
signature(from="AlignedReadTrack",
to="data.frame"): coerce the GRanges
object in the range slot into a regular data.frame.
Examples:
as(obj, "data.frame")
- displayPars
signature(x="AlignedReadTrack",
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="AlignedReadTrack",
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="AlignedReadTrack", 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="AlignedReadTrack", name="missing"):
alias for the displayPars method. See
settings for details on display parameters and
customization.
Examples:
getPar(obj)
- displayPars<-
signature(x="AlignedReadTrack",
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="AlignedReadTrack", value="character"):
set the single display parameter name to value. Note
that display parameters in the AlignedReadTrack 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="AlignedReadTrack", value="list"): set
display parameters by the values of the named list in
value. Note that display parameters in the
AlignedReadTrack 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="AlignedReadTrack"): 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="AlignedReadTrack"): return the value of
the name slot.
Usage:
names(x)
Examples:
names(obj)
- names<-
signature(x="AlignedReadTrack", value="character"):
set the value of the name slot.
Usage:
names<-(x, value)
Examples:
names(obj) <- "foo"
- coords
signature(ImageMap="AlignedReadTrack"): return the
coordinates from the internal image map.
Usage:
coords(ImageMap)
Examples:
coords(obj)
- tags
signature(x="AlignedReadTrack"): return the tags from the
internal image map.
Usage:
tags(x)
Examples:
tags(obj)
Display Parameters
The following display parameters are set for objects of class
AlignedReadTrack 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.
collapse=FALSE: collapse overlapping ranges and
aggregate the underlying data.
detail="coverage": the amount of detail to plot the
data. Either coverage to show the coverage only, or
reads to show individual reads. For large data sets the
latter can be very inefficient. Please note that reads is
only available when the object has been created with option
coverageOnly=FALSE.
fill="#0080ff": the fill color for the coverage
indicator.
size=NULL: the relative size of the track. Defaults
to size selection based on the underlying data. Can be overridden
in the plotTracks function.
type="histogram": the plot type, one or several in
c("p","l", "b", "a", "s", "g", "r", "S", "smooth", "histogram",
"mountain", "polygon", "h", "boxplot", "gradient", "heatmap",
"horizon"). See the 'Details' section in DataTrack
for more information on the individual plotting types.
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 AlignedReadTrack objects.
StackedTrack:
reverseStacking=FALSE: Logical flag. Reverse
the y-ordering of stacked items. I.e., features that are
plotted on the bottom-most stacks will be moved to the top-most
stack and vice versa.
stackHeight=0.75: Numeric between 0 and 1.
Controls the vertical size and spacing between stacked
elements. The number defines the proportion of the total
available space for the stack that is used to draw the glyphs.
E.g., a value of 0.5 means that half of the available vertical
drawing space (for each stacking line) is used for the glyphs,
and thus one quarter of the available space each is used for
spacing above and below the glyph. Defaults to 0.75.
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
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.
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 class is deprecated!
## Please use instead:
## - DataTrack
## - AnnotationTrack
## - AlignmentsTrack
## Below 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 Usage Arguments Value Objects from the Class Slots Extends Methods Display Parameters Author(s) See Also Examples
Description
DEPRECATED! This class and methods are deprecated, please use DataTrack,
AnnotationTrack or AlignmentsTrack instead.
A class to represent short sequences that have been aligned to a reference genome as they are typically generated in a next generation sequencing experiment.
Usage
1 2 |
Arguments
range |
An object of class
Alternatively, the |
start, end, width |
Integer vectors, giving the start and the end end coordinates for the individual track items, or their width. Two of the three need to be specified, and have to be of equal length or of length one, in which case this value will be recycled. Otherwise, the usual R recycling rules for vectors do not apply. |
strand |
Character vector, the strand information for the
individual track items. Needs to be of equal length as the
|
chromosome |
The chromosome on which the track's genomic ranges
are defined. A valid UCSC chromosome identifier. Please note that at
this stage only syntactic checking takes place, i.e., the argument
value needs to be a single integer, numeric character or a character
of the form |
genome |
The genome on which the track's ranges are defined. Usually this is a valid UCSC genome identifier, however this is not being formally checked at this point. |
stacking |
The stacking type for overlapping items of the
track. One in |
name |
Character scalar of the track's name used in the title panel when plotting. |
coverageOnly |
Instead of storing individual reads, just compute the coverage and store the resulting coverage vector. |
... |
Additional items which will all be interpreted as further display parameters. |
Value
The return value of the constructor function is a new object of class
AlignedReadTrack.
Objects from the Class
Objects can be created using the constructor function AlignedReadTrack.
Slots
coverage:Object of class
"list", a list of coverage vectors for the plus strand, the minus strand and for both strands combined.coverageOnly:Object of class
"logical", flag to determine whether the object stores read locations or the coverage vectors only.stacking:Object of class
"character", inherited from classStackedTrackstacks:Object of class
"environment", inherited from classStackedTrackrange:Object of class
GRanges, inherited from classRangeTrackchromosome:Object of class
"character", inherited from classRangeTrackgenome:Object of class
"character", inherited from classRangeTrackdp:Object of class
DisplayPars, inherited from classGdObjectname:Object of class
"character", inherited from classGdObjectimageMap:Object of class
ImageMap, inherited from classGdObject
Extends
Class "StackedTrack", directly.
Class "RangeTrack", by class "StackedTrack",
distance2.
Class "GdObject", by class "StackedTrack",
distance3.
Methods
In the following code chunks, obj is considered to be an object
of class AlignedReadTrack.
Exported in the name space:
- [
signature(x="AlignedReadTrack"): subset the items in theAlignedReadTrack. This is essentially similar to subsetting of theGRangesobject in therangeslot. For most applications, thesubsetmethod may be more appropriate. The operation is only supported for objects that still contain all the read locations, i.e.,coverageOnly=FALSE.Additional Arguments:
i: subsetting indices
Examples:
obj[1:5]
- subset
signature(x="AlignedReadTrack"): subset aAlignedReadTrackby coordinates and sort if necessary.Usage:
subset(x, from, to, sort=FALSE, stacks=FALSE)Additional Arguments:
from,to: the coordinates range to subset to.sort: sort the object after subsetting. Usually not necessary.stacks: recompute the stacking after subsetting which can be expensive and is not always necessary.
Examples:
subset(obj, from=10, to=20)subset(obj, from=10, to=20, sort=TRUE, stacks=FALSE)
- split
signature(x="AlignedReadTrack"): split anAlignedReadTrackobject by an appropriate factor vector (or another vector that can be coerced into one). The output of this operation is a list ofAlignedReadTrackobjects.Additional Arguments:
f: the splitting factor....: all further arguments are ignored.
Usage:
split(x, f, ...)Examples:
split(obj, c("a", "a", "b", "c", "a"))
- coverage
signature(x="AlignedReadTrack"): return the coverage vector for one of the strands, or the combined vector.Usage:
coverage(x, strand="*")Additional Arguments:
strand: the selector for the strand,+for the Watson strand,-for the Crick strand or*for both strands.
Examples:
coveraget(obj)coverage(obj, strand="-")
Internal methods:
- setCoverage
signature(GdObject="AlignedReadTrack"): recompute the coverage on the plus and minus strand as well as for the combined strands and update the respective slot.Usage:
setCoverage(GdObject)Examples:
setCoverage(obj)
- drawAxis
signature(GdObject="AlignedReadTrack"): add a y-axis to the title panel of a track.Usage:
drawAxis(GdObject, from, to, subset=FALSE, ...)Additional Arguments:
from,to: compute axis range from the data within a certain coordinates range only.subset: subset the object prior to calculating the axis ranges. Can be expensive and is not always needed....: all further arguments are ignored.
Examples:
Gviz:::drawAxis(obj)
- drawGD
signature(gdObject="AlignedReadTrack"): plot the object to a graphics device. The return value of this method is the input object, potentially updated during the plotting operation. Internally, there are two modes in which the method can be called. Either in 'prepare' mode, in which case no plotting is done but the object is preprocessed based on the available space, or in 'plotting' mode, in which case the actual graphical output is created. Since subsetting of the object can be potentially costly, this can be switched off in case subsetting has already been performed before or is not necessary.Usage:
drawGD(GdObject, minBase, maxBase, prepare=FALSE, subset=TRUE, ...)Additional Arguments:
minBase,maxBase: the coordinate range to plot.prepare: run method in preparation or in production mode.subset: subset the object to the visible region or skip the potentially expensive subsetting operation....: all further arguments are ignored.
Examples:
Gviz:::drawGD(obj)Gviz:::drawGD(obj, minBase=1, maxBase=100)Gviz:::drawGD(obj, prepare=TRUE, subset=FALSE)
- drawGrid
signature(GdObject="AlignedReadTrack"): superpose a grid on top of a track.Usage:
drawGrid(GdObject, from, to)Additional Arguments:
from,to: draw grid within a certain coordinates range. This needs to be supplied for the plotting function to know the current genomic coordinates.
Examples:
Gviz:::drawGrid(obj, from=10, to=100)
- initialize
signature(.Object="AligendReadTrack"): initialize the object.- show
signature(object="AlignedReadTrack"): show a human-readable summary of the object.
Inherited methods:
- stacking
signature(GdObject="AlignedReadTrack"): return the current stacking type.Usage:
stacking(GdObject)Examples:
stacking(obj)
- stacking<-
signature(GdObject="AlignedReadTrack", value="character"): set the object's stacking type to one inc(hide, dense, squish, pack,full).Usage:
stacking<-(GdObject, value)Additional Arguments:
value: replacement value.
Examples:
stacking(obj) <- "squish"
- setStacks
signature(GdObject="AlignedReadTrack"): recompute the stacks based on the available space and on the object's track items and stacking settings.Usage:
setStacks(GdObject, from, to)Additional Arguments:
from,to: compute stacking within a certain coordinates range. This needs to be supplied for the plotting function to know the current genomic coordinates.
Examples:
Gviz:::setStacks(obj)
- stacks
signature(GdObject="AlignedReadTrack"): return the stack indices for each track item.Usage:
stacks(GdObject)Examples:
Gviz:::stacks(obj)
- chromosome
signature(GdObject="AlignedReadTrack"): return the chromosome for which the track is defined.Usage:
chromosome(GdObject)Examples:
chromosome(obj)
- chromosome<-
signature(GdObject="AlignedReadTrack"): 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="AlignedReadTrack"): 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="AlignedReadTrack"): 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="AlignedReadTrack"): 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="AlignedReadTrack"): 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="AlignedReadTrack", 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 theAlignedReadTrack. SeegroupingorAnnotationTrackandGeneRegionTrackfor details.Usage:
feature<-(GdObject, value)Additional Arguments:
value: replacement value.
Examples:
feature(obj) <- c("a", "a", "b", "c", "a")
- genome
signature(x="AlignedReadTrack"): return the track's genome.Usage:
genome(x)Examples:
genome(obj)
- genome<-
signature(x="AlignedReadTrack"): 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="AlignedReadTrack"): return the number of items in the track.Usage:
length(x)Examples:
length(obj)
- range
signature(x="AlignedReadTrack"): return the genomic coordinates for the track as an object of classIRanges.Usage:
range(x)Examples:
range(obj)
- ranges
signature(x="AlignedReadTrack"): return the genomic coordinates for the track along with all additional annotation information as an object of classGRanges.Usage:
ranges(x)Examples:
ranges(obj)
- strand
signature(x="AlignedReadTrack"): 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="AlignedReadTrack"): 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="AlignedReadTrack"): return all additional annotation information except for the genomic coordinates for the track items as a data.frame.Usage:
values(x)Examples:
values(obj)
- coerce
signature(from="AlignedReadTrack", to="data.frame"): coerce theGRangesobject in therangeslot into a regular data.frame.Examples:
as(obj, "data.frame")
- displayPars
signature(x="AlignedReadTrack", 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="AlignedReadTrack", name="missing"): list the value of all available display parameters. Seesettingsfor details on display parameters and customization.Examples:
displayPars(obj)
- getPar
signature(x="AlignedReadTrack", name="character"): alias for thedisplayParsmethod. Seesettingsfor details on display parameters and customization.Usage:
getPar(x, name)Examples:
getPar(obj, "col")
- getPar
signature(x="AlignedReadTrack", name="missing"): alias for thedisplayParsmethod. Seesettingsfor details on display parameters and customization.Examples:
getPar(obj)
- displayPars<-
signature(x="AlignedReadTrack", 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="AlignedReadTrack", value="character"): set the single display parameternametovalue. Note that display parameters in theAlignedReadTrackclass 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="AlignedReadTrack", value="list"): set display parameters by the values of the named list invalue. Note that display parameters in theAlignedReadTrackclass 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="AlignedReadTrack"): 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="AlignedReadTrack"): return the value of thenameslot.Usage:
names(x)Examples:
names(obj)
- names<-
signature(x="AlignedReadTrack", value="character"): set the value of thenameslot.Usage:
names<-(x, value)Examples:
names(obj) <- "foo"
- coords
signature(ImageMap="AlignedReadTrack"): return the coordinates from the internal image map.Usage:
coords(ImageMap)Examples:
coords(obj)
- tags
signature(x="AlignedReadTrack"): return the tags from the internal image map.Usage:
tags(x)Examples:
tags(obj)
Display Parameters
The following display parameters are set for objects of class
AlignedReadTrack 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.
collapse=FALSE: collapse overlapping ranges and aggregate the underlying data.detail="coverage": the amount of detail to plot the data. Eithercoverageto show the coverage only, orreadsto show individual reads. For large data sets the latter can be very inefficient. Please note thatreadsis only available when the object has been created with optioncoverageOnly=FALSE.fill="#0080ff": the fill color for the coverage indicator.size=NULL: the relative size of the track. Defaults to size selection based on the underlying data. Can be overridden in theplotTracksfunction.type="histogram": the plot type, one or several inc("p","l", "b", "a", "s", "g", "r", "S", "smooth", "histogram", "mountain", "polygon", "h", "boxplot", "gradient", "heatmap", "horizon"). See the 'Details' section inDataTrackfor more information on the individual plotting types.
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 AlignedReadTrack objects.
StackedTrack:reverseStacking=FALSE: Logical flag. Reverse the y-ordering of stacked items. I.e., features that are plotted on the bottom-most stacks will be moved to the top-most stack and vice versa.stackHeight=0.75: Numeric between 0 and 1. Controls the vertical size and spacing between stacked elements. The number defines the proportion of the total available space for the stack that is used to draw the glyphs. E.g., a value of 0.5 means that half of the available vertical drawing space (for each stacking line) is used for the glyphs, and thus one quarter of the available space each is used for spacing above and below the glyph. Defaults to 0.75.
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 panelsfontcolor="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.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 22 23 24 25 26 27 | ## This class is deprecated!
## Please use instead:
## - DataTrack
## - AnnotationTrack
## - AlignmentsTrack
## Below 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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