AlignmentsTrack-class: AlignmentsTrack class and methods

In Gviz: Plotting data and annotation information along genomic coordinates

Description

A class to represent short sequences that have been aligned to a reference genome as they are typically generated in next generation sequencing experiments.

Usage

AlignmentsTrack(range=NULL, start=NULL, end=NULL, width=NULL, strand, 
                chromosome, genome, stacking="squish", id, cigar, mapq, flag,
                isize, groupid, status, md, seqs, name="AlignmentsTrack", 
                isPaired=TRUE, importFunction, referenceSequence,  ...)

Arguments

In the most common case AlignmentsTrack objects will be created directly from BAM files, and we strongly recommend to do this. A BAM file contains all the information that is needed to properly display the aligned reads, but more importantly, it allows to dynamically stream the data for the desired plotting range off the disk rather than having to load potentially gigantic amounts of data into memory upon object instantiation. That being said, there are other starting points to build AlignmentsTracks.

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 character string: the path to a BAM file containing the read alignments. To be precise, this will result in the instantiation of a ReferenceAlignmentsTrack object, but for the user this implementation detail should be of no concern. A GRanges object: the genomic ranges of the individual reads as well as the optional additional metadata columns id, cigar, mapq, flag, isize, groupid, status, md and seqs (see description of the individual function parameters below for details). Calling the constructor on a GRanges object without further arguments, e.g. AlignmentsTrack(range=obj) is equivalent to calling the coerce method as(obj, "AlignmentsTrack"). An IRanges object: almost identical to the GRanges case, except that the chromosome and strand information as well as all additional metadata has to be provided in the separate chromosome, strand, feature, group or id arguments, because it can not be directly encoded in an IRanges object. Note that none of those inputs are mandatory, and if not provided explicitely the more or less reasonable default values chromosome=NA and strand="*" are used. 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 it will be drawn from the separate chromosome or strand arguments. In addition, the id, cigar, mapq, flag, isize, groupid, status, md and seqs data can be provided as additional columns. The above comments about potential default values also apply here.
start, end, width	Integer vectors, giving the start and the 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 single value will be recycled. Otherwise, the usual R recycling rules for vectors do not apply here.
id	Character vector of read identifiers. Those identifiers have to be unique, i.e., each range representing a read needs to have a unique id.
cigar	A character vector of valid CIGAR strings describing details of the alignment. Typically those include alignment gaps or insertions and deletions, but also hard and soft clipped read regions. If missing, a fully mapped read without gaps or indels is assumed. Needs to be of equal length as the provided genomic coordinates, or of length 1.
mapq	A numeric vector of read mapping qualities. Needs to be of equal length as the provided genomic coordinates, or of length 1.
flag	A named integer vector of length 2, as is produced by Rsamtools::scanBamFlag(), used to filter out undesirable reads. If missing, all mapped reads will be included.
isize	A numeric vector of empirical insert sizes. This only applies if the reads are paired. Needs to be of equal length as the provided genomic coordinates, or of length 1. Currently not used.
groupid	A factor (or vector than can be coerced into one) defining the read pairs. Reads with the same groupid are considered to be mates. Please note that each read group may only have one or two members. Needs to be of equal length as the provided genomic coordinates, or of length 1.
status	A factor describing the mapping status of a read. Has to be one in mated, unmated or ambiguous. Needs to be of equal length as the provided genomic coordinates, or of length 1.
md	A character vector describing the mapping details. This is effectively and alternative to the CIGAR encoding and it removes the dependency on a reference sequence to figure out read mismatches. Needs to be of equal length as the provided genomic coordinates, or of length 1. Currently not used.
seqs	DNAStringSet of read sequences.
strand	Character vector, the strand information for the reads. It may be provided in the form + for the Watson strand, - for the Crick strand or * for either one of the two. Needs to be of equal length as the provided genomic coordinates, or of length 1. Please note that paired reads need to be on opposite strands, 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 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 construct 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.
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 input, 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 squish (make best use of the available space), dense (no stacking, collapse overlapping ranges), and hide (do not show any track items at all) are implemented.
name	Character scalar of the track's name used in the title panel when plotting.
isPaired	A logical scalar to determine whether the reads are paired or not. While this may be used to render paired-end data as single-end, the oppsite will typically not have any effect because the appropriate groupid settings will not be present. Thus setting isPaired to TRUE can usually be used to autodetect the pairing state of the input data.
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 a second argument selection with the desired plotting ranges. It has to return a proper GRanges object with all the necessary metadata columns set. A single default import function is already implemented in the package for BAM files.
referenceSequence	An optional SequenceTrack object containing the reference sequence against which the reads have been aligned. This is only needed when mismatch information has to be added to the plot (i.e., the showMismatchs display parameter is TRUE) because this is normally not encoded in the BAM file. If not provided through this argument, the plotTracks function is smart enough to detect the presence of a SequenceTrack object in the track list and will use that as a reference sequence.
...	Additional items which will all be interpreted as further display parameters. See settings and the "Display Parameters" section below for details.

Value

The return value of the constructor function is a new object of class AlignmentsTrack or ReferenceAlignmentsTrack.

Objects from the Class

Objects can be created using the constructor function AlignmentsTrack.

details

AlignmentTracks usually have two section: the coverage section on top showing a histogram of the read coverage, and the pile-up section below with the individual reads. Both can be toggled on or off using the type display parameter. If reference sequence has been provided either during object instantiation or with the track list to the call to plotTracks, sequence mismatch information will be shown in both sections: as a stacked histogram in the coverage plot and as colored boxes or characters (depending on available space) in for the pile-ups.

Slots

stackRanges:

Object of class "GRanges", the ranges of the precomputed mate or gaps stacks that should remain conmnected.

sequences:

Object of class "DNAStringSet", the processed read sequences.

referenceSequence:

Object of class "SequenceTrack", the reference sequence to which the reads have been aligned to.

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 AlignmentsTrack.

Exported in the name space:

[

signature(x="AlignmentsTrack"): subset the items in the AlignmentsTrack. 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: subsetting indices

Examples:

obj[1:5]

subset

signature(x="AlignmentsTrack"): subset a AlignmentsTrack 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="AlignmentsTrack"): split an AlignmentsTrack object by an appropriate factor vector (or another vector that can be coerced into one). The output of this operation is a list of AlignmentsTrack 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"))

Internal methods:

drawAxis

signature(GdObject="AlignmentsTrack"): 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="AlignmentsTrack"): 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)

initialize

signature(.Object="AligendReadTrack"): initialize the object.

show

signature(object="AlignmentsTrack"): show a human-readable summary of the object.

Inherited methods:

stacking

signature(GdObject="AlignmentsTrack"): return the current stacking type.

Usage:

stacking(GdObject)

Examples:

stacking(obj)

stacking<-

signature(GdObject="AlignmentsTrack", 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="AlignmentsTrack"): 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="AlignmentsTrack"): return the stack indices for each track item.

Usage:

stacks(GdObject)

Examples:

Gviz:::stacks(obj)

chromosome

signature(GdObject="AlignmentsTrack"): return the chromosome for which the track is defined.

Usage:

chromosome(GdObject)

Examples:

chromosome(obj)

chromosome<-

signature(GdObject="AlignmentsTrack"): 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="AlignmentsTrack"): 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="AlignmentsTrack"): 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="AlignmentsTrack"): 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="AlignmentsTrack"): 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="AlignmentsTrack", 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 AlignmentsTrack. 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="AlignmentsTrack"): return the track's genome.

Usage:

genome(x)

Examples:

genome(obj)

genome<-

signature(x="AlignmentsTrack"): 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="AlignmentsTrack"): return the number of items in the track.

Usage:

length(x)

Examples:

length(obj)

range

signature(x="AlignmentsTrack"): return the genomic coordinates for the track as an object of class IRanges.

Usage:

range(x)

Examples:

range(obj)

ranges

signature(x="AlignmentsTrack"): 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="AlignmentsTrack"): 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="AlignmentsTrack"): 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="AlignmentsTrack"): 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="AlignmentsTrack", to="data.frame"): coerce the GRanges object in the range slot into a regular data.frame.

Examples:

as(obj, "data.frame")

displayPars

signature(x="AlignmentsTrack", 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="AlignmentsTrack", 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="AlignmentsTrack", 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="AlignmentsTrack", name="missing"): alias for the displayPars method. See settings for details on display parameters and customization.

Examples:

getPar(obj)

displayPars<-

signature(x="AlignmentsTrack", 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="AlignmentsTrack", value="character"): set the single display parameter name to value. Note that display parameters in the AlignmentsTrack 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="AlignmentsTrack", value="list"): set display parameters by the values of the named list in value. Note that display parameters in the AlignmentsTrack 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="AlignmentsTrack"): 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="AlignmentsTrack"): return the value of the name slot.

Usage:

names(x)

Examples:

names(obj)

names<-

signature(x="AlignmentsTrack", value="character"): set the value of the name slot.

Usage:

names<-(x, value)

Examples:

names(obj) <- "foo"

coords

signature(ImageMap="AlignmentsTrack"): return the coordinates from the internal image map.

Usage:

coords(ImageMap)

Examples:

coords(obj)

tags

signature(x="AlignmentsTrack"): 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 AlignmentsTrack upon instantiation, unless one or more of them have already been set by one of the optional sub-class initializers, which always get precedence over these global defaults. See settings for details on setting graphical parameters for tracks.

alpha.mismatch=1: Numeric scalar between 0 and 1. The transparency of the mismatch base information.

alpha.reads=0.5: Numeric scalar between 0 and 1. The transparency of the individual read icons. Can be used to indicate overlapping regions in read pairs. Only on supported devices.

cex=0.7: Numeric Scalar. The global character expansion factor.

cex.mismatch=NULL: Numeric Scalar. The character expansion factor for the mismatch base letters.

col="#808080": Integer or character scalar. The default color of all line elements.

col.coverage=NULL: Integer or character scalar. The line color for the coverage profile.

col.deletion="#000000": Integer or character scalar. The color of the line that is bridging the deleted regions in alignments.

col.gap="#808080" (Aliases: col.gap): Integer or character scalar. The color of the line that is bridging the gap regions in gapped alignments.

col.insertion="#984EA3": Integer or character scalar. The color of the line that highlighting insertions in alignments.

col.mates="#E0E0E0" (Aliases: col.mate): Integer or character scalar. The color of the line that is connecting two paired reads.

col.mismatch="#808080": Integer or character scalar. The box color around mismatch bases.

col.reads=NULL: Integer or character scalar. The box color around reads.

col.sashimi=NULL: Integer or character scalar. The line color for sashimi plots.

collapse=FALSE: Logical scalar. Do not perform any collapsing of overlapping elements. Currently not supported.

coverageHeight=0.1: Numeric scalar. The height of the coverage region of the track. Can either be a value between 0 and 1 in which case it is taken as a relative height, or a positive value greater 1 in which case it is interpreted as pixels.

fill="#BABABA": Integer or character scalar. The default fill color of all plot elements.

fill.coverage=NULL: Integer or character scalar. The fill color for the coverage profile.

fill.reads=NULL: Integer or character scalar. The fill color for the read icons.

fontface.mismatch=2: Integer scalar. The font face for mismatch bases.

lty=1: Integer or character scalar. The default type of all line elements.

lty.coverage=NULL: Integer or character scalar. The line type of the coverage profile.

lty.deletion=NULL: Integer or character scalar. The type of the line that is bridging the deleted regions in alignments.

lty.gap=NULL (Aliases: lty.gap): Integer or character scalar. The type of the line that is bridging the gap regions in gapped alignments.

lty.insertion=NULL: Integer or character scalar. The type of the line that highlighting insertions in alignments.

lty.mates=NULL (Aliases: lty.mate): Integer or character scalar. The type of the line that is connecting two paired reads.

lty.mismatch=NULL: Integer or character scalar. The box line type around mismatch bases.

lty.reads=NULL: Integer or character scalar. The box line type around mismatch reads.

lwd=1: Integer scalar. The default width of all line elements.

lwd.coverage=NULL: Integer or character scalar. The line width of the coverage profile.

lwd.deletion=NULL: Integer scalar. The width of the line that is bridging the deleted regions in alignments.

lwd.gap=NULL (Aliases: lwd.gap): Integer scalar. The width of the line that is bridging the gap regions in gapped alignments.

lwd.insertion=NULL: Integer scalar. The width of the line that highlighting insertions in alignments.

lwd.mates=NULL (Aliases: lwd.mate): Integer scalar. The width of the line that is connecting two paired reads.

lwd.mismatch=NULL: Integer scalar. The box line width around mismatch bases.

lwd.reads=NULL: Integer scalar. The box line width around reads.

lwd.sashimiMax=10: Integer scalar. The maximal width of the line in sashimi plots.

max.height=10: Integer scalar. The maximum height of an individual read in pixels. Can be used in combination with min.height to control the read and stacking appearance.

min.height=5: Integer scalar. The minimum height of an individual read in pixels. Can be used in combination with max.height to control the read and stacking appearance.

minCoverageHeight=50: Integer scalar. The minimum height of the coverage section. Uselful in combination with a relative setting of coverageHeight.

minSashimiHeight=50: Integer scalar. The minimum height of the sashimi section. Uselful in combination with a relative setting of sashimiHeight.

noLetters=FALSE: Logical scalar. Always plot colored boxes for mismatch bases regardles of the available space.

sashimiFilter=NULL: GRanges object. Only junctions which overlap equally with sashimiFilter GRanges are shown. Default NULL, no filtering.

sashimiFilterTolerance=0: Integer scalar. Only used in combination with sashimiFilter. It allows to include junctions whose starts/ends are within specified distance from sashimiFilter GRanges. This is useful for cases where the aligner did not place the junction reads precisely. Default 0L , no tolerance.

sashimiHeight=0.1: Integer scalar. The height of the sashimi part of the track. Can either be a value between 0 and 1 in which case it is taken as a relative height, or a positive value greater 1 in which case it is interpreted as pixels.

sashimiScore=1: Integer scalar. The minimum number of reads supporting the junction.

sashimiStrand="*": Integer scalar. Only reads which have the specified strand are considered to count the junctions.

sashimiTransformation=NULL: Function. Applied to the junction score vector prior to plotting. The function should accept exactly one input argument and its return value needs to be a numeric vector of identical length as the input data.

showIndels=FALSE: Logical scalar. Consider insertions and deletions in coverage and pile-up. Default is FALSE. If set to TRUE the deletions defined in CIGAR string are not considered in coverage plot. The deletions are displayed as bridging lines in pile-up track. Insertions are shown as vertical bars.

showMismatches=TRUE: Logical scalar. Add mismatch information, either as individual base letters or using color coded bars. This implies that the reference sequence has been provided, either to the class constructor or as part of the track list.

size=NULL: Numeric scalar. The size of the track. Defaults to automatic sizing.

transformation=NULL: Function. Applied to the coverage vector prior to plotting. The function should accept exactly one input argument and its return value needs to be a numeric Rle of identical length as the input data.

type=c("coverage", "pileup"): Character vactor. The type of information to plot. For coverage a coverage plot, potentially augmented by base mismatch information, for sashimi a sashimi plot, showing the juctions, and for pileup the pileups of the individual reads. These three can be combined.

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 AlignmentsTrack 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.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.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.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.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.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

AnnotationTrack

DataTrack

DisplayPars

GdObject

GeneRegionTrack

GRanges

ImageMap

IRanges

RangeTrack

SequenceTrack

StackedTrack

collapsing

grouping

panel.grid

plotTracks

settings

Examples

## Creating objects
afrom <- 2960000
ato <- 3160000
alTrack <- AlignmentsTrack(system.file(package="Gviz", "extdata",
"gapped.bam"), isPaired=TRUE)
plotTracks(alTrack, from=afrom, to=ato, chromosome="chr12")

## Omit the coverage or the pile-ups part
plotTracks(alTrack, from=afrom, to=ato, chromosome="chr12",
type="coverage")
plotTracks(alTrack, from=afrom, to=ato, chromosome="chr12",
type="pileup")

## Including sequence information with the constructor
if(require(BSgenome.Hsapiens.UCSC.hg19)){
strack <- SequenceTrack(Hsapiens, chromosome="chr21")
afrom <- 44945200
ato <- 44947200
alTrack <- AlignmentsTrack(system.file(package="Gviz", "extdata",
"snps.bam"), isPaired=TRUE, referenceSequence=strack)
plotTracks(alTrack, chromosome="chr21", from=afrom, to=ato)

## Including sequence information in the track list
alTrack <- AlignmentsTrack(system.file(package="Gviz", "extdata",
"snps.bam"), isPaired=TRUE)
plotTracks(c(alTrack, strack), chromosome="chr21", from=44946590,
to=44946660)
}

Gviz documentation built on March 16, 2021, 6:01 p.m.