Usage
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, ...)Arguments
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:
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
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.