GeneRegionTrack-class {Gviz} | R Documentation |
A class to hold gene model data for a genomic region.
GeneRegionTrack(range=NULL, rstarts=NULL, rends=NULL, rwidths=NULL, strand, feature, exon, transcript, gene, symbol, chromosome, genome, stacking="squish", name="GeneRegionTrack", start=NULL, end=NULL, importFunction, stream=FALSE, ...)
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 The different input options for
|
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 |
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 |
rends |
An integer vector of the end coordinates for the actual
gene model items. Both |
rwidths |
An integer vector of widths for the actual gene model
items. This can be used instead of either |
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 |
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 |
strand |
Character vector, the strand information for the
individual track exons. It may be provided in the form |
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
|
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 |
chromosome |
The chromosome on which the track's genomic ranges
are defined. A valid UCSC chromosome identifier if
|
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 |
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. |
importFunction |
A user-defined function to be used to import the
data from a file. This only applies when the |
stream |
A logical flag indicating that the user-provided import
function can deal with indexed files and knows how to process the
additional |
... |
Additional items which will all be interpreted as further
display parameters. See |
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
:
identifiers are stored in the exon column of the
GRanges
object in the range
slot. Data
may be extracted using the exon
method.
identifiers are stored in the transcript
column of the GRanges
object. Data may be
extracted using the transcript
method.
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.
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.
The return value of the constructor function is a new object of class
GeneRegionTrack
.
Objects can be created using the constructor function
GeneRegionTrack
.
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
:Class "AnnotationTrack"
, directly.
Class "StackedTrack"
, by class "AnnotationTrack",
distance2.
Class "RangeTrack"
, by class "AnnotationTrack",
distance3.
Class "GdObject"
, by class "AnnotationTrack",
distance4.
In the following code chunks, obj
is considered to be an object of class GeneRegionTrack
.
Exported in the name space:
signature(gdObject="GeneRegionTrack")
: extract
the group membership for all track items.
Usage:
group(GdObject)
Examples:
group(obj)
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")
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)
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")
signature(GdObject="GeneRegionTrack")
: Extract
the exon identifiers for all exons in the gene models.
Usage:
exon(GdObject)
Examples:
exon(obj)
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)
signature(GdObject="GeneRegionTrack")
: Extract
the gene identifiers for all gene models.
Usage:
gene(GdObject)
Examples:
gene(obj)
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])
signature(GdObject="GeneRegionTrack")
: Extract
the human-readble gene symbol for all gene models.
Usage:
symbol(GdObject)
Examples:
symbol(obj)
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]
signature(GdObject="GeneRegionTrack")
:
Extract the transcript identifiers for all transcripts in the
gene models.
Usage:
transcript(GdObject)
Examples:
transcript(obj)
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:
signature(from="GeneRegionTrack",
to="UCSCData")
: coerce to a UCSCData
object for export to
the UCSC genome browser.
Examples:
as(obj, "UCSCData")
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.
Usage:
collapseTrack(GdObject, diff=.pxResolution(coord="x"))
Additional Arguments:
diff
: the minimum pixel width to display,
everything below that will be inflated to a width of
diff
.
Examples:
Gviz:::collapseTrack(obj)
signature(.Object="GeneRegionTrack")
:
initialize the object
signature(object="GeneRegionTrack")
: show a
human-readable summary of the object
Inherited methods:
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.
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)
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)
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)
signature(GdObject="GeneRegionTrack")
: return
the current stacking type.
Usage:
stacking(GdObject)
Examples:
stacking(obj)
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"
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]
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)
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"
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)
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
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)
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)
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")
signature(x="GeneRegionTrack")
: return the track's genome.
Usage:
genome(x)
Examples:
genome(obj)
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"
signature(x="GeneRegionTrack")
: return the number
of items in the track.
Usage:
length(x)
Examples:
length(obj)
signature(x="GeneRegionTrack")
: return the genomic
coordinates for the track as an object of class
IRanges
.
Usage:
range(x)
Examples:
range(obj)
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)
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"))
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)
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) <- "+"
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)
signature(from="GeneRegionTrack",
to="data.frame")
: coerce the GRanges
object in the range
slot into a regular data.frame.
Examples:
as(obj, "data.frame")
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)
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")
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)
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")
signature(x="GeneRegionTrack", name="missing")
:
alias for the displayPars
method. See
settings
for details on display parameters and
customization.
Examples:
getPar(obj)
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)
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")
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))
signature(x="GeneRegionTrack")
: return the value of
the name
slot.
Usage:
names(x)
Examples:
names(obj)
signature(x="GeneRegionTrack", value="character")
:
set the value of the name
slot.
Usage:
names<-(x, value)
Examples:
names(obj) <- "foo"
signature(ImageMap="GeneRegionTrack")
: return the
coordinates from the internal image map.
Usage:
coords(ImageMap)
Examples:
coords(obj)
signature(x="GeneRegionTrack")
: return the tags from the
internal image map.
Usage:
tags(x)
Examples:
tags(obj)
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
collapse==TRUE
. See collapsing
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.
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
.
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.
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 DataTrack
s 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 DataTrack
s and when display parameter
grid==TRUE
.
lwd.grid=1
: Numeric scalar. Default line width
for grid lines, both when type=="g"
in DataTrack
s
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.
Florian Hahne, Steve Lianoglou
## The empty object GeneRegionTrack() ## Load some sample data data(cyp2b10) ## Construct the object grTrack <- GeneRegionTrack(start=26682683, end=26711643, rstart=cyp2b10$start, rends=cyp2b10$end, chromosome=7, genome="mm9", transcript=cyp2b10$transcript, gene=cyp2b10$gene, symbol=cyp2b10$symbol, feature=cyp2b10$feature, exon=cyp2b10$exon, name="Cyp2b10", strand=cyp2b10$strand) ## Directly from the data.frame grTrack <- GeneRegionTrack(cyp2b10) ## From a TxDb object if(require(GenomicFeatures)){ samplefile <- system.file("extdata", "hg19_knownGene_sample.sqlite", package="GenomicFeatures") txdb <- loadDb(samplefile) GeneRegionTrack(txdb) GeneRegionTrack(txdb, chromosome="chr6", start=35000000, end=40000000) } ## Plotting plotTracks(grTrack) ## Track names names(grTrack) names(grTrack) <- "foo" plotTracks(grTrack) ## Subsetting and splitting subTrack <- subset(grTrack, from=26700000, to=26705000) length(subTrack) subTrack <- grTrack[transcript(grTrack)=="ENSMUST00000144140"] split(grTrack, transcript(grTrack)) ## Accessors start(grTrack) end(grTrack) width(grTrack) position(grTrack) width(subTrack) <- width(subTrack)+100 strand(grTrack) strand(subTrack) <- "-" chromosome(grTrack) chromosome(subTrack) <- "chrX" genome(grTrack) genome(subTrack) <- "hg19" range(grTrack) ranges(grTrack) ## Annotation identifier(grTrack) identifier(grTrack, "lowest") identifier(subTrack) <- "bar" feature(grTrack) feature(subTrack) <- "foo" exon(grTrack) exon(subTrack) <- letters[1:2] gene(grTrack) gene(subTrack) <- "bar" symbol(grTrack) symbol(subTrack) <- "foo" transcript(grTrack) transcript(subTrack) <- c("foo", "bar") chromosome(subTrack) <- "chr7" plotTracks(subTrack) values(grTrack) ## Grouping group(grTrack) group(subTrack) <- "Group 1" transcript(subTrack) plotTracks(subTrack) ## Collapsing transcripts plotTracks(grTrack, collapseTranscripts=TRUE, showId=TRUE, extend.left=10000, shape="arrow") ## Stacking stacking(grTrack) stacking(grTrack) <- "dense" plotTracks(grTrack) ## coercion as(grTrack, "data.frame") as(grTrack, "UCSCData") ## HTML image map coords(grTrack) tags(grTrack) grTrack <- plotTracks(grTrack)$foo coords(grTrack) tags(grTrack)