AlignmentsTrack-class {Gviz} | R Documentation

## AlignmentsTrack class and methods

### 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 alignemnts 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 numeric vector of flag values. Needs to be of equal length as the provided genomic coordinates, or of length 1. Currently not used.
`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.gap="#808080"` `(Aliases: col.gap)`: Integer or character scalar. The color of the line that is bridging the gap regions in gapped 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.gap=NULL` `(Aliases: lty.gap)`: Integer or character scalar. The type of the line that is bridging the gap regions in gapped 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.gap=NULL` `(Aliases: lwd.gap)`: Integer scalar. The width of the line that is bridging the gap regions in gapped 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.

  `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 `DataTrack`s 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 `DataTrack`s 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 `DataTrack`s 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`

`GRanges`

`GdObject`

`GeneRegionTrack`

`IRanges`

`ImageMap`

`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)
    }

[Package Gviz version 1.30.3 Index]