AnnotationTrack-class: AnnotationTrack class and methods
In ivanek/Gviz: Plotting data and annotation information along genomic coordinates

AnnotationTrack-class

R Documentation

AnnotationTrack class and methods

Description

A fairly generic track object for arbitrary genomic range annotations, with the option of grouped track items. The extended DetailsAnnotationTrack provides a more flexible interface to add user-defined custom information for each range.

Usage

## S4 method for signature 'AnnotationTrack'
initialize(.Object, ...)

## S4 method for signature 'ReferenceAnnotationTrack'
initialize(
  .Object,
  stream,
  reference,
  mapping = list(),
  args = list(),
  defaults = list(),
  ...
)

AnnotationTrack(
  range = NULL,
  start = NULL,
  end = NULL,
  width = NULL,
  feature,
  group,
  id,
  strand,
  chromosome,
  genome,
  stacking = "squish",
  name = "AnnotationTrack",
  fun,
  selectFun,
  importFunction,
  stream = FALSE,
  ...
)

DetailsAnnotationTrack(...)

## S4 method for signature 'DetailsAnnotationTrack'
initialize(.Object, fun, selectFun, ...)

## S4 method for signature 'AnnotationTrack'
group(GdObject)

## S4 replacement method for signature 'AnnotationTrack,character'
group(GdObject) <- value

## S4 method for signature 'AnnotationTrack'
identifier(GdObject, type = .dpOrDefault(GdObject, "groupAnnotation", "group"))

## S4 replacement method for signature 'AnnotationTrack,character'
identifier(GdObject) <- value

## S4 method for signature 'AnnotationTrack'
setStacks(GdObject, recomputeRanges = TRUE)

## S4 method for signature 'AnnotationTrack'
consolidateTrack(
  GdObject,
  hasAxis = FALSE,
  hasTitle = .dpOrDefault(GdObject, "showTitle", TRUE),
  title.width = NULL,
  ...
)

## S4 method for signature 'AnnotationTrack'
collapseTrack(GdObject, diff = .pxResolution(coord = "x"), xrange)

## S4 method for signature 'AnnotationTrack'
subset(
  x,
  from = NULL,
  to = NULL,
  sort = FALSE,
  stacks = FALSE,
  use.defaults = TRUE,
  ...
)

## S4 method for signature 'ReferenceAnnotationTrack'
subset(x, from, to, chromosome, ...)

## S4 method for signature 'AnnotationTrack'
drawGD(GdObject, minBase, maxBase, prepare = FALSE, subset = TRUE, ...)

## S4 method for signature 'DetailsAnnotationTrack'
drawGD(GdObject, minBase, maxBase, prepare = FALSE, ...)

## S4 method for signature 'AnnotationTrack'
show(object)

## S4 method for signature 'ReferenceAnnotationTrack'
show(object)

Arguments

`...`	Additional items which will all be interpreted as further display parameters. See settings and the "Display Parameters" section below for details.
`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 `ReferenceAnnotationTrack` object which will grab the necessary data on the fly during each plotting operation.
`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 `GRanges` object: the genomic ranges for the `Annotation` track as well as the optional additional metadata columns `feature`, `group` and `id` (see description of the individual function parameters below for details). Calling the constructor on a `GRanges` object without further arguments, e.g. `AnnotationTrack(range=obj)` is equivalent to calling the coerce method `as(obj, "AnnotationTrack")`. A `GRangesList` object: this is very similar to the previous case, except that the grouping information that is part of the list structure is preserved in the `AnnotationTrack`. I.e., all the elements within one list item receive the same group id. For consistency, there is also a coercion method from `GRangesLists` `as(obj,"AnnotationTrack")`. 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 `IRange` object. Note that none of those inputs are mandatory, and if not provided explicitly 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 `feature`, `group` and `id` data can be provided as additional columns. The above comments about potential default values also apply here. A `character` scalar: in this case the value of the `range` argument is considered to be a file path to an annotation file on disk. A range of file types are supported by the `Gviz` package as identified by the file extension. See the `importFunction` documentation below for further details.
`start, end, width`	Integer vectors, giving the start and the end 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.
`feature`	Factor (or other vector that can be coerced into one), giving the feature types for the individual track items. 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 colour. See `grouping` for details. Needs to be of equal length as the provided genomic coordinates, or of length 1.
`group`	Factor (or other vector that can be coerced into one), giving the group memberships for the individual track items. When plotting to the device, all items in the same group will be connected. See `grouping` for details. Needs to be of equal length as the provided genomic coordinates, or of length 1.
`id`	Character vector of track item identifiers. When plotting to the device, it's value will be used as the identifier tag if the display parameter `showFeatureId=TRUE`. Needs to be of equal length as the provided genomic ranges, or of length 1.
`strand`	Character vector, the strand information for the individual track items. 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 grouped items need to be on the same strand, 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.
`fun`	A function that is being called for each entry in the `AnnotationTrack` object. See section 'Details' and 'Examples' for further information. When called internally by the plotting machinery, a number of arguments are automatically passed on to this function, and the user needs to make sure that they can all be digested (i.e., either have all of them as formal named function arguments, or gobble up everything that is not needed in `...`). These arguments are: `start`: the genomic start coordinate of the range item. `end`: the genomic end coordinates of the range item. `strand`: the strand information for the range item. `chromosome`: the chromosome of the range item. `identifier`: the identifier of the range item, i.e., the result of calling `identifier(DetailsAnnotationTrack, lowest=TRUE)`. Typically those identifiers are passed on to the object constructor during instantiation as the `id` argument. `index`: a counter enumerating the ranges. The `AnnotationTrack` object is sorted internally for visibility, and the `index` argument refers to the index of plotting. `GdObject`: a reference to the currently plotted `DetailsAnnotationTrack` object. `GdObject.original`: a reference to the `DetailsAnnotationTrack` before any processing like item collapsing has taken place. Essentially, this is the track object as it exists in your working environment. Additional arguments can be passed to the plotting function by means of the `detailsFunArgs` argument (see below). Note that the plot must use grid graphics (e.g. function in the 'lattice' package or low-level grid functions). To access a data object such a matrix or data frame within the function you can either store it as a variable in the global environment or, to avoid name space conflicts, you can make it part of the function environment by means of a closure. Alternatively, you may want to explicitely stick it into an environment or pass it along in the `detailsFunArgs` list. To figure out in your custom plotting function which annotation element is currently being plotted you can either use the identifier which has to be unique for each range element, or you may want to use the genomic position (start/end/strand/chromosome) e.g. if the data is stored in a `GRanges` object.
`selectFun`	A function that is being called for each entry in the `AnnotationTrack` object with exactly the same arguments as in `fun`. The purpose of this function is to decide for each track element whether details should be drawn, and consequently it has to return a single logical scalar. If the return value is `TRUE`, details will be drawn for the item, if it is `FALSE`, the details strip for the item is omitted.
`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`, `bed`, `bam`.

Value

The return value of the constructor function is a new object of class AnnotationTrack or of class DetailsAnnotationTrack, depending on the constructor arguments. Typically the user will not have to be troubled with this distinction and can rely on the constructor to make the right choice.

Functions

initialize(AnnotationTrack): Show method.
ReferenceAnnotationTrack-class: The file-based version of the AnnotationTrack-class.
initialize(ReferenceAnnotationTrack): Initialize.
AnnotationTrack(): Constructor function for AnnotationTrack-class
DetailsAnnotationTrack-class: directly extends AnnotationTrack.
DetailsAnnotationTrack(): Constructor function for DetailsAnnotationTrack-class

The DetailsAnnotationTrack class directly extends AnnotationTrack. The purpose of this track type is to add an arbitrarily detailed plot section (typically consisting of additional quantitative data) for each range element of an AnnotationTrack. This allows a locus wide view of annotation elements together with any kind of details per feature or element that may for instance provide insight on how some complex quantitative measurements change according to their position in a locus. If the quantitative data is too complex for a DataTrack e.g. because it requires extra space or a trellis-like representation, a DetailsAnnotationTrack can be used instead. Example: An AnnotationTrack shows the positions of a number of probes from a microarray, and you want a histogram of the signal intensity distribution derived from all samples at each of these probe location. Another example usage would be to show for each element of an AnnotationTrack an xy-plot of the signal against some clinical measurement such as blood pressure. The limitation for applications of this type of track is basically only the available space of the device you are plotting to.

This flexibility is possible by utilizing a simple function model to perform all the detailed plotting. The functionality of this plotting function fun is totally up to the user, and the function environment is prepared in a way that all necessary information about the plotted annotation feature is available. To restrict the details section to only selected number of annotation features one can supply another function selectFun, which decides for each feature separately whether details are available or not. Finally, an arbitrary number of additional arguments can be passed on to these two function by means of the detailsFunArgs display parameter. This is expected to be a named list, and all list elements are passed along to the plotting function fun and to the selector function selectFun as additional named arguments. Please note that some argument names like start, end or identifier are reserved and can not be used in the detailsFunArgs list. For examples of plotting functions, see the 'Examples' section.
initialize(DetailsAnnotationTrack): Initialize.
group(AnnotationTrack): extract the group membership for all track items.
group(GdObject = AnnotationTrack) <- value: 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.
identifier(AnnotationTrack): return track item identifiers. Depending on the setting of the optional argument lowest, these are either the group identifiers or the individual item identifiers.
identifier(GdObject = AnnotationTrack) <- value: 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<-⁠.
setStacks(AnnotationTrack): Recompute the stacks based on the available space and on the object's track items and stacking settings.
consolidateTrack(AnnotationTrack): Consolidate. Determine whether there is group label annotation or not, and add this information as the internal display parameter .__hasAnno. Precompute the grouped ranges together with optional labels in order to determine the correct plotting range later.
collapseTrack(AnnotationTrack): 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.
subset(AnnotationTrack): subset a AnnotationTrack by coordinates and sort if necessary.
subset(ReferenceAnnotationTrack): subset a ReferenceAnnotationTrack by coordinates and sort if necessary.
drawGD(AnnotationTrack): 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.
drawGD(DetailsAnnotationTrack): 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.
show(AnnotationTrack): Show method.
show(ReferenceAnnotationTrack): Show method.

Slots

dp: Object of DisplayPars-class, the display settings controlling the look and feel of a track. See settings for details on setting graphical parameters for tracks.
name: Object of class character, a human-readable name for the track that will be used in the track's annotation panel if necessary.
imageMap: Object of ImageMap-class, containing optional information for an HTML image map. This will be created by the drawGD methods when the track is plotted to a device and is usually not set by the user.
range: Object of class GRanges, the genomic ranges of the track items as well as additional annotation information in its elementMetaData slot. Please not that the slot is actually implemented as a class union between GRanges and IRanges to increase efficiency, for instance for DataTrack objects. This usually does not concern the user.
chromosome: Object of class character, the chromosome on which the track is defined. There can only be a single chromosome for one track. For certain subclasses, the space of allowed chromosome names is limited (e.g., only those chromosomes that exist for a particular genome). Throughout the package, chromosome name have to be entered either as a single integer scalar or as a character scalar of the form chrXYZ, where XYZ may be an arbitrary character string.
genome: Object of class character, the genome for which the track is defined. For most sub-classes this has to be valid UCSC genome identifier, however this may not always be formally checked upon object instantiation.
stacking: Object of class character, the stacking type of overlapping items on the final plot. One in c(hide, dense, squish, pack,full). Currently, only hide (do not show the track items at all), squish (make best use of the available space) and dense (no stacking at all) are implemented.
stacks: Object of class numeric, holding the stack indices for each track item. This slot is usually populated by calling the setStacks method upon plotting, since the correct stacking is a function of the available plotting space.
fun: A function that is being called for each AnnotationTrack element to plot details.
selectFun: A function that is being called for each AnnotationTrack element to decide whether details need to be plotted.

Objects from the class

Objects can be created using the constructor function AnnotationTrack.

Author(s)

Florian Hahne, Arne Mueller

Examples

## An empty object
AnnotationTrack()

## Construct from individual arguments
st <- c(2000000, 2070000, 2100000, 2160000)
ed <- c(2050000, 2130000, 2150000, 2170000)
str <- c("-", "+", "-", "-")
gr <- c("Group1", "Group2", "Group1", "Group3")

annTrack <- AnnotationTrack(
    start = st, end = ed, strand = str, chromosome = 7,
    genome = "hg19", feature = "test", group = gr,
    id = paste("annTrack item", 1:4),
    name = "generic annotation", stacking = "squish"
)

## Or from a data.frame
df <- data.frame(
    start = st, end = ed, strand = str, id = paste("annTrack item", 1:4),
    feature = "test", group = gr
)
annTrack <- AnnotationTrack(
    range = df, genome = "hg19", chromosome = 7,
    name = "generic annotation", stacking = "squish"
)

## Or from a GRanges object
gr <- GRanges(
    seqnames = "chr7", range = IRanges(start = df$start, end = df$end),
    strand = str
)
genome(gr) <- "hg19"
mcols(gr) <- df[, -(1:3)]
annTrack <- AnnotationTrack(
    range = gr, name = "generic annotation",
    stacking = "squish"
)

## Finally from a GRangesList
grl <- split(gr, values(gr)$group)
AnnotationTrack(grl)


## Plotting
plotTracks(annTrack)

## Track names
names(annTrack)
names(annTrack) <- "foo"
plotTracks(annTrack)

## Subsetting and splitting
subTrack <- subset(annTrack, to = 2155000)
length(subTrack)
subTrack[1:2]
split(annTrack, c(1, 2, 1, 2))

## Accessors
start(annTrack)
end(annTrack)
width(annTrack)
position(annTrack)
width(subTrack) <- width(subTrack) + 1000

strand(annTrack)
strand(subTrack) <- "-"

chromosome(annTrack)
chromosome(subTrack) <- "chrX"

genome(annTrack)
genome(subTrack) <- "mm9"

range(annTrack)
ranges(annTrack)

## Annotation
identifier(annTrack)
identifier(annTrack, "lowest")
identifier(subTrack) <- "bar"

feature(annTrack)
feature(subTrack) <- "foo"

values(annTrack)

## Grouping
group(annTrack)
group(subTrack) <- "Group 1"
chromosome(subTrack) <- "chr7"
plotTracks(subTrack)

## Stacking
stacking(annTrack)
stacking(annTrack) <- "dense"
plotTracks(annTrack)

## coercion
as(annTrack, "data.frame")
as(annTrack, "UCSCData")

## HTML image map
coords(annTrack)
tags(annTrack)
annTrack <- plotTracks(annTrack)$foo
coords(annTrack)
tags(annTrack)

## DetailsAnnotationTrack
library(lattice) # need to use grid grapics

## generate two random distributions per row (probe/feature)
## the difference between the distributions increases from probe 1 to 4
m <- matrix(c(rgamma(400, 1)), ncol = 100)
m[, 51:100] <- m[, 51:100] + 0:3
## rownames must be accessible by AnnotationTrack element identifier
rownames(m) <- identifier(annTrack, "lowest")

## create a lattice density plot for the values (signals) of the two groups
## as the chart must be placed into a pre-set grid view port we have to use
## print without calling plot.new! Note, use a common prefix for all lattice.
## Avoid wasting space by removing y-axis decorations.

## Note, in this example 'm' will be found in the environment the 'details'
## function is defined in. To avoid overwriting 'm' you should use a closure
## or environment to access 'm'.
details <- function(identifier, ...) {
    d <- data.frame(signal = m[identifier, ], group = rep(c("grp1", "grp2"), each = 50))
    print(densityplot(~signal,
        group = group, data = d, main = identifier,
        scales = list(draw = FALSE, x = list(draw = TRUE)), ylab = "", xlab = "",
    ), newpage = FALSE, prefix = "plot")
}

deTrack <- AnnotationTrack(
    range = gr, genome = "hg19", chromosome = 7,
    name = "generic annotation with details per entry", stacking = "squish",
    fun = details, details.ratio = 1
)

plotTracks(deTrack)

set.seed(1234)
deTrack <- AnnotationTrack(
    range = gr, genome = "hg19", chromosome = 7,
    name = "generic annotation with details per entry",
    stacking = "squish", fun = details,
    details.ratio = 1, selectFun = function(...) {
        sample(c(FALSE, TRUE), 1)
    }
)

plotTracks(deTrack)

ivanek/Gviz documentation built on Nov. 20, 2023, 8:16 p.m.