Since GeneRegionTrack objects are essentially just a specific
type of AnnotationTrack objects, their
constructors are quite similar. However, in the case of the
GeneRegionTrack certain assumptions are made about the type of
grouping on different levels (see the Details section for more
information). The natural representation for gene models in the
Bioconductor world are TxDb objects, and
we tried to make it as straight forward as possible to create
GeneRegionTracks starting from those. Building the object from
individual function arguments is of course still possible.
range
An optional meta argument to handle the different input types. If
the range argument is missing, all the relevant information
to create the object has to be provided as individual function
arguments (see below).
The different input options for range are:
A TxDb object: all the necessary gene model
information including exon locations, transcript groupings and
associated gene ids are contained in TxDb
objects, and the coercion between the two is almost completely
automated. If desired, the data to be fetched from the
TxDb object can be restricted using the
constructor's chromosome, start and end
arguments. See below for details. A direct coercion method
as(obj, "GeneRegionTrack") is also available. A nice
added benefit of this input option is that the UTR and coding
region information that is part of the original
TxDb object is retained in the
GeneRegionTrack.
A GRanges object: the genomic ranges for the
GeneRegion track as well as the optional additional
metadata columns feature,
transcript, gene, exon and symbol
(see description of the individual function parameters below for
details). Calling the constructor on a GRanges object
without further arguments, e.g.
GeneRegionTrack(range=obj) is equivalent to calling the
coerce method as(obj, "GeneRegionTrack").
A GRangesList object: this is very similar to the
previous case, except that the grouping information that is part
of the list structure is preserved in the
GeneRegionTrack. I.e., all the elements within one list
item receive the same group id. For consistancy, there is also a
coercion method from GRangesListsas(obj,
"GeneRegionTrack"). Please note that unless the necessary
information about gene ids, symbols, etc. is present in the
individual GRanges meta data slots, the object will not
be particularly useful, because all the identifiers will be set
to a common default value.
An IRanges object: almost identical
to the GRanges case, except that the chromosome and
strand information as well as all additional data has to be
provided in the separate chromosome, strand,
feature, transcript, symbol, exon or
gene arguments, because it can not be directly encoded in
an IRanges object. Note that only the former two are
mandatory (if not provided explicitely the more or less
reasonable default values chromosome=NA and
strand=* are used, but not providing information about
the gene-to-transcript relationship or the human-readble symbols
renders a lot of the class' functionality useles.
A data.frame object: the data.frame needs to
contain at least the two mandatory columns start and
end with the range coordinates. It may also contain a
chromosome and a strand column with the chromosome
and strand information for each range. If missing, this
information will be drawn from the constructor's
chromosome or strand arguments. In addition, the
feature, exon, transcript, gene and
symbol data can be provided as columns in the
data.frame. The above comments about potential default
values also apply here.
A character scalar: in this case the value of the
range argument is considered to be a file path to an
annotation file on disk. A range of file types are supported by
the Gviz package as identified by the file extension. See
the importFunction documentation below for further
details.
start, end
An integer scalar with the genomic start or end
coordinate for the gene model range. If those are missing, the
default value will automatically be the smallest (or largest) value,
respectively in rstarts and rends for the currently
active chromosome. When building a GeneRegionTrack from a
TxDb object, these arguments can be used to subset
the desired annotation data by genomic coordinates. Please note this
in that case the chromosome parameter must also be set.
rstarts
An integer vector of the start coordinates for the
actual gene model items, i.e., for the individual exons. The
relationship between exons is handled via the gene and
transcript factors. Alternatively, this can be a vector of
comma-separated lists of integer coordinates, one vector item for
each transcript, and each comma-separated element being the start
location of a single exon within that transcript. Those lists will
be exploded upon object instantiation and all other annotation
arguments will be recycled accordingly to regenerate the
exon/transcript/gene relationship structure. This implies the
approriate number of items in all annotation and coordinates
arguments.
rends
An integer vector of the end coordinates for the actual
gene model items. Both rstarts and rends have to be of
equal length.
rwidths
An integer vector of widths for the actual gene model
items. This can be used instead of either rstarts or
rends to specify the range coordinates.
feature
Factor (or other vector that can be coerced into one),
giving the feature types for the individual track exons. When
plotting the track to the device, if a display parameter with the
same name as the value of feature is set, this will be used
as the track item's fill color. Additionally, the feature type
defines whether an element in the GeneRegionTrack is
considered to be coding or non-coding. The details section as well
as the section about the thinBoxFeature display parameter
further below has more information on this. See also
grouping for details.
exon
Character vector of exon identifiers. It's values will be
used as the identifier tag when plotting to the device if the
display parameter showExonId=TRUE.
strand
Character vector, the strand information for the
individual track exons. It may be provided in the form + for
the Watson strand, - for the Crick strand or * for
either one of the two. Please note that all items within a single
gene or transcript model need to be on the same strand, and
erroneous entries will result in casting of an error.
transcript
Factor (or other vector that can be coerced into
one), giving the transcript memberships for the individual track
exons. All items with the same transcript identifier will be
visually connected when plotting to the device. See
grouping for details. Will be used as labels when
showId=TRUE, and geneSymbol=FALSE.
gene
Factor (or other vector that can be coerced into one),
giving the gene memberships for the individual track exons.
symbol
A factor with human-readable gene name aliases which
will be used as labels when showId=TRUE, and
geneSymbol=TRUE.
chromosome
The chromosome on which the track's genomic ranges
are defined. A valid UCSC chromosome identifier if
options(ucscChromosomeNames=TRUE). Please note that in this
case only syntactic checking takes place, i.e., the argument value
needs to be an 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. If not provided here, the constructor will
try to build the chromosome information based on the available
inputs, and as a last resort will fall back to the value
chrNA. Please note that by definition all objects in the
Gviz package can only have a single active chromosome at a
time (although internally the information for more than one
chromosome may be present), and the user has to call the
chromosome<- replacement method in order to change to a
different active chromosome. When creating a GeneRegionTrack
from a TxDb object, the value of this parameter can
be used to subset the data to fetch only transcripts from a single
chromosome.
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. If not provided
here the constructor will try to extract this information from the
provided inputs, and eventually will fall back to the default value
of NA.
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.
importFunction
A user-defined function to be used to import the
data from a file. This only applies when the range argument
is a character string with the path to the input data file. The
function needs to accept an argument x containing the file
path and has to return a proper GRanges object with all the
necessary metadata columns set. A set of default
import functions is already implemented in the package for a number
of different file types, and one of these defaults will be picked
automatically based on the extension of the input file name. If the
extension can not be mapped to any of the existing import function,
an error is raised asking for a user-defined import function via
this argument. Currently the following file types can be imported
with the default functions: gff, gff1, gff2,
gff3, gtf.
stream
A logical flag indicating that the user-provided import
function can deal with indexed files and knows how to process the
additional selection argument when accessing the data on
disk. This causes the constructor to return a
ReferenceGeneRegionTrack object which will grab the necessary data
on the fly during each plotting operation.
...
Additional items which will all be interpreted as further
display parameters. See settings and the "Display
Parameters" section below for details.
Details
A track containing all gene models in a particular region. The data
are usually fetched dynamially from an online data store, but it is
also possible to manully construct objects from local
data. Connections to particular online data sources should be
implemented as sub-classes, and GeneRegionTrack is just the
commone denominator that is being used for plotting later on. There
are several levels of data associated to a GeneRegionTrack:
exon level:
identifiers are stored in the exon column of the
GRanges object in the range slot. Data
may be extracted using the exon method.
transcript level:
identifiers are stored in the transcript
column of the GRanges object. Data may be
extracted using the transcript method.
gene level:
identifiers are stored in the gene column of the
GRanges object, more human-readable versions
in the symbol column. Data may be extracted using the gene
or the symbol methods.
transcript-type level:
information is stored in the feature
column of the GRanges object. If a display
parameter of the same name is specified, the software will use its
value for the coloring.
GeneRegionTrack objects also know about coding regions and
non-coding regions (e.g., UTRs) in a transcript, and will indicate
those by using different shapes (wide boxes for all coding regions,
thinner boxes for non-coding regions). This is archived by setting the
feature values of the object for non-coding elements to one of
the options that are provided in the thinBoxFeature display
parameters. All other elements are considered to be coding elements.
Value
The return value of the constructor function is a new object of class
GeneRegionTrack.
Objects from the class
Objects can be created using the constructor function
GeneRegionTrack.
Slots
start:
Object of class "numeric", the start
coordinates of the annotation range. The coorrdinates for the
individual gene model items are stored in the range slot.
end:
Object of class "numeric", the end
coordinates of the annotation range. The corrdinates for the
individual gene model items are stored in the range slot.
stacking:
Object of class "character",
inherited from class StackedTrack
stacks:
Object of class "numeric",
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 "AnnotationTrack", directly.
Class "StackedTrack", by class "AnnotationTrack",
distance2.
Class "RangeTrack", by class "AnnotationTrack",
distance3.
Class "GdObject", by class "AnnotationTrack",
distance4.
Methods
In the following code chunks, obj is considered to be an object of class GeneRegionTrack.
Exported in the name space:
group
signature(gdObject="GeneRegionTrack"): extract
the group membership for all track items.
Usage:
group(GdObject)
Examples:
group(obj)
group<-
signature(gdObject="GeneRegionTrack",
value="character"): replace the grouping information for track
items. The replacement value must be a factor of appropriate
length or another vector that can be coerced into such.
Usage:
group<-(GdObject, value)
Examples:
group(obj) <- c("a", "a", "b", "c", "a")
identifier
signature(gdObject="GeneRegionTrack"):
return track item identifiers. Depending on the setting of the
optional argument lowest, these are either the group
identifiers or the individual item identifiers.
Usage:
identifier(GdObject, lowest=FALSE)
Additional Arguments:
lowest: return the lowest-level identifier, i.e.,
the item IDs, or the higher level group IDs which do not have to
be unqiue.
Examples:
identifier(obj, lowest=FALSE)
identifier<-
signature(gdObject="GeneRegionTrack",
value="character"): Set the track item identifiers. The
replacement value has to be a character vector of appropriate
length. This always replaces the group-level identifiers, so
essentially it is similar to groups<-.
Usage:
identifier<-(GdObject, value)
Examples:
identifier(obj) <- c("foo", "bar")
exon
signature(GdObject="GeneRegionTrack"): Extract
the exon identifiers for all exons in the gene models.
Usage:
exon(GdObject)
Examples:
exon(obj)
exon<-
signature(GdObject="GeneRegionTrack",
value="character"): replace the exon identifiers for all exons in
the gene model. The replacement value must be a character of
appropriate length or another vector that can be coerced into
such.
Usage:
exon<-(GdObject, value)
Examples:
exon(obj) <- paste("Exon", 1:5)
gene
signature(GdObject="GeneRegionTrack"): Extract
the gene identifiers for all gene models.
Usage:
gene(GdObject)
Examples:
gene(obj)
gene<-
signature(GdObject="GeneRegionTrack",
value="character"): replace the gene identifiers for all gene
models. The replacement value must be a character of
appropriate length or another vector that can be coerced into
such.
Usage:
gene<-(GdObject, value)
Examples:
gene(obj) <- paste("Gene", LETTERS[1:5])
symbol
signature(GdObject="GeneRegionTrack"): Extract
the human-readble gene symbol for all gene models.
Usage:
symbol(GdObject)
Examples:
symbol(obj)
symbol<-
signature(GdObject="GeneRegionTrack",
value="character"): replace the human-readable gene symbol for
all gene models. The replacement value must be a character of
appropriate length or another vector that can be coerced into
such.
Usage:
gene<-(GdObject, value)
Examples:
symbol(obj) <- letters[1:5]
transcript
signature(GdObject="GeneRegionTrack"):
Extract the transcript identifiers for all transcripts in the
gene models.
Usage:
transcript(GdObject)
Examples:
transcript(obj)
transcript<-
signature(GdObject="GeneRegionTrack",
value="character"): replace the transcript identifiers for
all transcripts in the gene model. The replacement value must
be a character of appropriate length or another vector that
can be coerced into such.
Usage:
transcript<-(GdObject, value)
Examples:
transcript(obj) <- paste("Exon", 1:5)
Internal methods:
coerce
signature(from="GeneRegionTrack",
to="UCSCData"): coerce to a UCSCData object for export to
the UCSC genome browser.
Examples:
as(obj, "UCSCData")
collapseTrack
signature(GdObject="GeneRegionTrack"):
preprocess the track before plotting. This will collapse
overlapping track items based on the available resolution and
increase the width and height of all track objects to a minimum
value to avoid rendering issues. See collapsing for
details.
diff: the minimum pixel width to display,
everything below that will be inflated to a width of
diff.
Examples:
Gviz:::collapseTrack(obj)
initialize
signature(.Object="GeneRegionTrack"):
initialize the object
show
signature(object="GeneRegionTrack"): show a
human-readable summary of the object
Inherited methods:
drawGD
signature(GdObject="GeneRegionTrack"): 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.
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="GeneRegionTrack"): superpose a grid on top of a track.
Usage:
drawGrid(GdObject, from, to)
Additional Arguments:
from, to: integer scalars, 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)
setStacks
signature(GdObject="GeneRegionTrack"):
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: integer scalars, 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, from=1, to=100)
stacking
signature(GdObject="GeneRegionTrack"): return
the current stacking type.
Usage:
stacking(GdObject)
Examples:
stacking(obj)
stacking<-
signature(GdObject="GeneRegionTrack",
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"
stacks
signature(GdObject="GeneRegionTrack"): return
the stack indices for each track item.
Usage:
stacks(GdObject)
Examples:
Gviz:::stacks(obj)
[
signature(x="GeneRegionTrack", i="ANY", j="ANY",
drop="ANY"): subset the items in the GeneRegionTrack
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="GeneRegionTrack"):
return the currently active chromosome for which the track is
defined. For consistancy with other Bioconductor packages, the
isActiveSeq alias is also provided.
Usage:
chromosome(GdObject)
Examples:
chromosome(obj)
chromosome<-
signature(GdObject="GeneRegionTrack"):
replace the value of the track's active chromosome. This has to
be a valid UCSC chromosome identifier or an integer or character
scalar that can be reasonably coerced into one, unless
options(ucscChromosomeNames=FALSE). For consistancy with
other Bioconductor packages, the isActiveSeq<- alias is
also provided.
Usage:
chromosome<-(GdObject, value)
Additional Arguments:
value: replacement value.
Examples:
chromosome(obj) <- "chr12"
start, end, width
signature(x="GeneRegionTrack"): 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="GeneRegionTrack"):
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="GeneRegionTrack"): 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="GeneRegionTrack"): return the
grouping information for track items. For certain sub-classes,
groups may be indicated by different color schemes when
plotting. See grouping for details.
Usage:
feature(GdObject)
Examples:
feature(obj)
feature<-
signature(gdObject="GeneRegionTrack",
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 GeneRegionTrack. See grouping
for details.
Usage:
feature<-(GdObject, value)
Additional Arguments:
value: replacement value.
Examples:
feature(obj) <- c("a", "a", "b", "c", "a")
genome
signature(x="GeneRegionTrack"): return the track's genome.
Usage:
genome(x)
Examples:
genome(obj)
genome<-
signature(x="GeneRegionTrack"): 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="GeneRegionTrack"): return the number
of items in the track.
Usage:
length(x)
Examples:
length(obj)
range
signature(x="GeneRegionTrack"): return the genomic
coordinates for the track as an object of class
IRanges.
Usage:
range(x)
Examples:
range(obj)
ranges
signature(x="GeneRegionTrack"): 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="GeneRegionTrack"): split a
GeneRegionTrack 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 GeneRegionTrack.
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="GeneRegionTrack"): 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="GeneRegionTrack"): 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="GeneRegionTrack"): 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="GeneRegionTrack",
to="data.frame"): coerce the GRanges
object in the range slot into a regular data.frame.
Examples:
as(obj, "data.frame")
subset
signature(x="GeneRegionTrack"): subset a
GeneRegionTrack 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)
displayPars
signature(x="GeneRegionTrack",
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="GeneRegionTrack",
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="GeneRegionTrack", 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="GeneRegionTrack", name="missing"):
alias for the displayPars method. See
settings for details on display parameters and
customization.
Examples:
getPar(obj)
displayPars<-
signature(x="GeneRegionTrack",
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="GeneRegionTrack", value="character"):
set the single display parameter name to value. Note
that display parameters in the GeneRegionTrack 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="GeneRegionTrack", value="list"): set
display parameters by the values of the named list in
value. Note that display parameters in the
GeneRegionTrack 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))
names
signature(x="GeneRegionTrack"): return the value of
the name slot.
Usage:
names(x)
Examples:
names(obj)
names<-
signature(x="GeneRegionTrack", value="character"):
set the value of the name slot.
Usage:
names<-(x, value)
Examples:
names(obj) <- "foo"
coords
signature(ImageMap="GeneRegionTrack"): return the
coordinates from the internal image map.
Usage:
coords(ImageMap)
Examples:
coords(obj)
tags
signature(x="GeneRegionTrack"): 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
GeneRegionTrack 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.
min.distance=0: Numeric scalar. The minimum pixel
distance before collapsing range items, only if
codecollapse==TRUE. See codelinkcollapsing for
details. Note that a value larger than 0 may lead to UTR regions
being merged to CDS regions, which in most cases is not particularly
useful.
col=NULL: Character or integer scalar. The border
color for all items. Defaults to using the same color as in
fill, also taking into account different track
features.
fill="orange": Character or integer scalar. The fill
color for untyped items. This is also used to connect grouped
items. See grouping for details.
geneSymbols=TRUE: Logical scalar. Use human-readable
gene symbols or gene IDs for the transcript annotation.
shape=c("smallArrow", "box"): Character scalar. The
shape in which to display the track items. Currently only
box, arrow, ellipse, and smallArrow
are implemented.
showExonId=FALSE: Logical scalar. Control whether
to plot the individual exon identifiers.
collapseTranscripts=FALSE: Logical or character
scalar. Can be one in gene, longest, shortest
or meta. Merge all
transcripts of the same gene into one single gene
model. In the case of gene (or TRUE), this will only keep the start location of the
first exon and the end location of the last exon from all
transcripts of the gene. For shortest and longest,
only the longest or shortest transcript model is retained. For
meta, a meta-transcript containing the union of all exons
is formed (essentially identical to the operation
reduce(geneModel)).
thinBoxFeature=c("utr", "ncRNA", "utr3", "utr5",
"miRNA", "lincRNA"): Character vector. A listing of feature
types that should be drawn with thin boxes. Typically those
are non-coding elements.
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 GeneRegionTrack objects.
AnnotationTrack:
cex=1: Numeric scalar. The font expansion factor
for item identifiers.
cex.group=0.6: Numeric scalar. The font expansion
factor for the group-level annotation.
col="transparent": Character or integer scalar.
The border color for all track items.
col.line="darkgray": Character scalar. The color used for
connecting lines between grouped items. Defaults to a dark gray,
but if set to NULL the same color as for the first item in
the group is used.
fontcolor="white": Character or integer scalar.
The font color for item identifiers.
fontcolor.group="#808080": Character or integer
scalar. The font color for the group-level annotation.
fontface=1: Integer scalar. The font face for
item identifiers.
fontface.group=2: Numeric scalar. The font face
for the group-level annotation.
fontfamily="sans": Character scalar. The font
family for item identifiers.
fontsize=12: Numeric scalar. The font size for
item identifiers.
lex=1: Numeric scalar. The line expansion factor
for all track items. This is also used to connect grouped
items. See grouping for details.
lineheight=1: Numeric scalar. The font line
height for item identifiers.
lty="solid": Character or integer scalar. The
line type for all track items. This is also used to connect
grouped items. See grouping for details.
lwd=1: Integer scalar. The line width for all
track items. This is also used to connect grouped items. See
grouping for details.
rotation=0: Numeric scalar. The degree of text
rotation for item identifiers.
showFeatureId=FALSE: Logical scalar. Control
whether to plot the individual track item identifiers.
showId=FALSE: Logical scalar. Control whether
to annotate individual groups.
showOverplotting=FALSE: Logical scalar. Use a
color gradient to show the amount of overplotting for collapsed
items. This implies that collapse==TRUE
size=1: Numeric scalar. The relative size of
the track. Can be overridden in the plotTracks
function.
mergeGroups=FALSE: Logical scalar. Merge fully
overlapping groups if collapse==TRUE.
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.
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 panels.
col.border.title="transparent": Integer or character
scalar. The border color for the title panels.
lwd.border.title=1: Integer scalar. The border
width for the title panels.
cex.axis=NULL: Numeric scalar. The expansion
factor for the axis annotation. Defaults to NULL, in
which case it is computed 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.axis="white": Integer or character scalar.
The font and line color for the y axis, if any.
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.symbol=NULL: Integer or character scalar.
Default colors for plot symbols. Usually the same as the
global col parameter.
col.title="white": Integer or character scalar.
The font color for the title panels.
collapse=TRUE: Boolean controlling wether to
collapse the content of the track to accomodate the minimum
current device resolution. See collapsing for
details.
fontface.title=2: Integer or character scalar.
The font face for the title panels.
fontfamily.title="sans": Integer or character
scalar. The font family for the title panels.
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.
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.grid=1: Numeric scalar. Default line width
for grid lines, both when type=="g" in DataTracks
and when display parameter grid==TRUE.
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.
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.