AnnotationTrack-class: AnnotationTrack class and methods

In Gviz: Plotting data and annotation information along genomic coordinates

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

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

Arguments

AnnotationTrack object can be created from a variety of different inputs in order to nicely embed the package into the existing Bioconductor landscape. Since the main components of this class are essentially genomic ranges, the obvious Bioconductor representation is most likely a GRanges object, or, for grouped elements, a GRangesList. However, in certain cases it may be desirable to build the object from individual function arguments.

range	An optional meta argument to handle the different input types. If the range argument is missing, all the relevant information to create the object has to be provided as individual function arguments (see below). The different input options for range are: 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 consistancy, 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 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 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 color. 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.
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.
...	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 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.

Objects from the class

Objects can be created using the constructor function AnnotationTrack.

Details

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 accoring 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 preassure. 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 separatly 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.

Slots

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

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.

Additional display parameters are being inherited from the StackedTrack parent class.

Extends

Class "StackedTrack", directly.

Class "RangeTrack", by class "StackedTrack", distance 2.

Class "GdObject", by class "StackedTrack", distance3.

DetailsAnnotationTrack directly extends AnnotationTrack.

Methods

In the following code chunks, obj is considered to be an object of class AnnotationTrack or DetailsAnnotationTrack.

Exported in the name space:

group

signature(GdObject="AnnotationTrack"): extract the group membership for all track items.

Usage:

group(GdObject)

Examples:

group(obj)

group<-

signature(GdObject="AnnotationTrack", value="character"): replace the grouping information for track items. The replacement value must be a factor of appropriate length or another vector that can be coerced into such.

Usage:

group<-(GdObject, value)

Examples:

group(obj) <- c("a", "a", "b", "c", "a")

identifier

signature(GdObject="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.

Usage:

identifier(GdObject, lowest=FALSE)

Additional Arguments:

lowest: return the lowest-level identifier, i.e., the item IDs, or the higher level group IDs which do not have to be unqiue.

Examples:

identifier(obj)

identifier(obj, lowest=TRUE)

identifier<-

signature(GdObject="AnnotationTrack", value="character"): Set the track item identifiers. The replacement value has to be a character vector of appropriate length. This always replaces the group-level identifiers, so essentially it is similar to groups<-.

Usage:

identifier<-(GdObject, value)

Examples:

identifier(obj) <- c("foo", "bar")

Internal methods:

coerce

signature(from="AnnotationTrack", to="UCSCData"): coerce to a UCSCData object for export to the UCSC genome browser.

Examples:

as(obj, "UCSCData")

collapseTrack

signature(GdObject="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.

Usage:

collapseTrack(GdObject, diff=.pxResolution(coord="x"))

Additional Arguments:

diff: the minimum pixel width to display, everything below that will be inflated to a width of diff.

Examples:

Gviz:::collapseTrack(obj)

drawGD

signature(GdObject="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.

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)

drawGrid

signature(GdObject="AnnotationTrack"): superpose a grid on top of a track.

Usage:

drawGrid(GdObject, from, to)

Additional Arguments:

from, to: integer scalars, draw grid within a certain coordinates range. This needs to be supplied for the plotting function to know the current genomic coordinates.

Examples:

Gviz:::drawGrid(obj, from=10, to=100)

setStacks

signature(GdObject="AnnotationTrack"): recompute the stacks based on the available space and on the object's track items and stacking settings.

Usage:

setStacks(GdObject, from, to)

Additional Arguments:

from, to: integer scalars, compute stacking within a certain coordinates range. This needs to be supplied for the plotting function to know the current genomic coordinates.

Examples:

Gviz:::setStacks(obj, from=1, to=100)

initialize

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

show

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

Inherited methods:

stacking

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

Usage:

stacking(GdObject)

Examples:

stacking(obj)

stacking<-

signature(GdObject="AnnotationTrack", 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"

stacks

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

Usage:

stacks(GdObject)

Examples:

Gviz:::stacks(obj)

[

signature(x="AnnotationTrack", i="ANY", j="ANY", drop="ANY"): subset the items in the AnnotationTrack object. This is essentially similar to subsetting of the GRanges object in the range slot. For most applications, the subset method may be more appropriate.

Additional Arguments:

i, j: subsetting indices, j is ignored.

drop: argument is ignored.

Examples:

obj[1:5]

chromosome

signature(GdObject="AnnotationTrack"): return the currently active chromosome for which the track is defined. For consistancy with other Bioconductor packages, the isActiveSeq alias is also provided.

Usage:

chromosome(GdObject)

Examples:

chromosome(obj)

chromosome<-

signature(GdObject="AnnotationTrack"): replace the value of the track's active chromosome. This has to be a valid UCSC chromosome identifier or an integer or character scalar that can be reasonably coerced into one, unless options(ucscChromosomeNames=FALSE). For consistancy with other Bioconductor packages, the isActiveSeq<- alias is also provided.

Usage:

chromosome<-(GdObject, value)

Additional Arguments:

value: replacement value.

Examples:

chromosome(obj) <- "chr12"

start, end, width

signature(x="AnnotationTrack"): 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="AnnotationTrack"): 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="AnnotationTrack"): 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="AnnotationTrack"): return the grouping information for track items. For certain sub-classes, groups may be indicated by different color schemes when plotting. See grouping for details.

Usage:

feature(GdObject)

Examples:

feature(obj)

feature<-

signature(gdObject="AnnotationTrack", 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 AnnotationTrack. See grouping for details.

Usage:

feature<-(GdObject, value)

Additional Arguments:

value: replacement value.

Examples:

feature(obj) <- c("a", "a", "b", "c", "a")

genome

signature(x="AnnotationTrack"): return the track's genome.

Usage:

genome(x)

Examples:

genome(obj)

genome<-

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

Usage:

length(x)

Examples:

length(obj)

range

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

Usage:

range(x)

Examples:

range(obj)

ranges

signature(x="AnnotationTrack"): 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)

split

signature(x="AnnotationTrack"): split a AnnotationTrack object by an appropriate factor vector (or another vector that can be coerced into one). The output of this operation is a list of objects of the same class as the input object, all inheriting from class AnnotationTrack.

Usage:

split(x, f, ...)

Additional Arguments:

f: the splitting factor.

...: all further arguments are ignored.

Examples:

split(obj, c("a", "a", "b", "c", "a"))

strand

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

Examples:

as(obj, "data.frame")

subset

signature(x="AnnotationTrack"): subset a AnnotationTrack by coordinates and sort if necessary.

Usage:

subset(x, from, to, sort=FALSE, ...)

Additional Arguments:

from, to: the coordinates range to subset to.

sort: sort the object after subsetting. Usually not necessary.

...: additional arguments are ignored.

Examples:

subset(obj, from=10, to=20, sort=TRUE)

displayPars

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

Examples:

getPar(obj)

displayPars<-

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

names

signature(x="AnnotationTrack"): return the value of the name slot.

Usage:

names(x)

Examples:

names(obj)

names<-

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

Usage:

names<-(x, value)

Examples:

names(obj) <- "foo"

coords

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

Usage:

coords(ImageMap)

Examples:

coords(obj)

tags

signature(x="AnnotationTrack"): 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 AnnotationTrack 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.

arrowHeadMaxWidth=40: Numeric scalar. The maximum width of the arrow head in pixels if shape is arrow.

arrowHeadWidth=30: Numeric scalar. The width of the arrow head in pixels if shape is fixedArrow.

cex=1: Numeric scalar. The font expansion factor for item identifiers.

cex.group=0.6: Numeric scalar. The font expansion factor for the group-level annotation.

col="transparent": Character or integer scalar. The border color for all track items.

col.line="darkgray": Character scalar. The color used for connecting lines between grouped items. Defaults to a light gray, but if set to NULL the same color as for the first item in the group is used.

featureAnnotation=NULL: Character scalar. Add annotation information to the individual track elements. This can be a value in id, group or feature. Defaults to id. Only works if showFeatureId is not FALSE.

fill="lightblue": Character or integer scalar. The fill color for untyped items. This is also used to connect grouped items. See grouping for details.

fontcolor.group="#808080" (Aliases: fontcolor.group): Character or integer scalar. The font color for the group-level annotation.

fontcolor.item="white" (Aliases: fontcolor.item): Character or integer scalar. The font color for item identifiers.

fontface.group=2: Numeric scalar. The font face for the group-level annotation.

fontfamily.group="sans": Character scalar. The font family for the group-level annotation.

fontsize.group=12: Numeric scalar. The font size for the group-level annotation.

groupAnnotation=NULL: Character scalar. Add annotation information as group labels. This can be a value in id, group or feature. Defaults to group. Only works if showId is not FALSE.

just.group="left" (Aliases: just.group): Character scalar. the justification of group labels. Either left, right, above or below.

lex=1: Numeric scalar. The line expansion factor for all track items. This is also used to connect grouped items. See grouping for details.

lineheight=1: Numeric scalar. The font line height for item identifiers.

lty="solid": Character or integer scalar. The line type for all track items. This is also used to connect grouped items. See grouping for details.

lwd=1: Integer scalar. The line width for all track items. This is also used to connect grouped items. See grouping for details.

mergeGroups=FALSE: Logical scalar. Merge fully overlapping groups if collapse==TRUE.

min.height=3: Numeric scalar. The minimum range height in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See collapsing for details. For feathered bars indicating the strandedness of grouped items this also controls the height of the arrow feathers.

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.

rotation=0: Numeric scalar. The degree of text rotation for item identifiers.

rotation.group=0: Numeric scalar. The degree of text rotation for group labels.

rotation.item=0: Numeric scalar. The degree of text rotation for item identifiers.

shape="arrow": Character scalar. The shape in which to display the track items. Currently only box, arrow, fixedArrow, ellipse, and smallArrow are implemented.

showFeatureId=FALSE: Logical scalar. Control whether to plot the individual track item identifiers.

showId=FALSE: Logical scalar. Control whether to annotate individual groups.

showOverplotting=FALSE: Logical scalar. Use a color gradient to show the amount of overplotting for collapsed items. This implies that collapse==TRUE

size=1: Numeric scalar. The relative size of the track. Can be overridden in the plotTracks function.

DetailsAnnotationTrack adds the following additional display parameters:

details.minWidth=100: Numeric scalar. The minium width in pixels for a details panel, if less space is available no details are plotted.

details.ratio=Inf: Numeric scalar. By default, the plotting method tries to fill all available space of the details panel tiles. Depending on the dimensions of your plot and the number of tiles this may lead to fairly stretched plots. Restricting the ration of width over height can help to fine tune for somewhat more sane graphics in these cases. Essentially this adds some white space in between individual tiles to force the desired ratio. Together with the size and details.size arguments, which control the vertical extension of the whole track and of the details section, this allows for some fairly generic resizing of the tiles.

details.size=0.5: Numeric scalar. The fraction of vertical space of the track used for the details section.

detailsBorder.col="darkgray": Character or integer scalar. Line color of the border.

detailsBorder.fill="transparent": Character or integer scalar. Background color of the border.

detailsBorder.lty="solid": Character or integer scalar. Line type of the border around each details panel.

detailsBorder.lwd=1: Integer scalar. Line width of the border.

detailsConnector.cex=1: Numeric scalar. Relative size of the connector's end points.

detailsConnector.col="darkgray": Character or integer scalar. Color of the line connecting the AnnotstionTrack item with its details panel.

detailsConnector.lty="dashed": Character or integer scalar. Type of connecting line.

detailsConnector.lwd=1: Integer scalar. Line width of the connector.

detailsConnector.pch=20: Integer scalar. Type of the connector's ends.

detailsFunArgs=character(0): List.Additional arguments that get passed on the the details plotting function.

groupDetails=FALSE: Logial scalar. Plot details for feature groups rather than for individual features.

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 AnnotationTrack 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.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

collapse=TRUE: Boolean controlling whether to collapse the content of the track to accomodate the minimum current device resolution. See collapsing for details.

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.

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.

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.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, Arne Mueller

See Also

DisplayPars

GdObject

GRanges

GRangesList

ImageMap

IRanges

RangeTrack

StackedTrack

collapsing

DataTrack

grouping

panel.grid

plotTracks

settings

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)

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