\name{AnnotationTrack-class} \Rdversion{1.1} \docType{class} \alias{AnnotationTrack-class} \alias{AnnotationTrack} \alias{DetailsAnnotationTrack-class} \alias{DetailsAnnotationTrack} \alias{initialize,DetailsAnnotationTrack-method} \alias{coerce,AnnotationTrack,UCSCData-method} \alias{collapseTrack,AnnotationTrack-method} \alias{drawGD,AnnotationTrack-method} \alias{drawGrid,AnnotationTrack-method} \alias{group} \alias{group,AnnotationTrack-method} \alias{group<-} \alias{group<-,AnnotationTrack,character-method} \alias{identifier,AnnotationTrack-method} \alias{identifier<-,AnnotationTrack,character-method} \alias{identifier} \alias{identifier<-} \alias{initialize,AnnotationTrack-method} \alias{setStacks,AnnotationTrack-method} \alias{show,AnnotationTrack-method} \alias{subset,AnnotationTrack-method} \title{AnnotationTrack class and methods} \description{ A fairly generic track object for arbitrary genomic range annotations, with the option of grouped track items. The extended \code{DetailsAnnotationTrack} provides a flexible interface to add user-defined custom information for each range. } \section{Objects from the class}{ Objects can be created using the constructor function \code{AnnotationTrack}. } \usage{ AnnotationTrack(range=NULL, start=NULL, end=NULL, width=NULL, feature, group, id, strand="*", chromosome, genome, stacking="squish", name="AnnotationTrack", fun, selectFun, ...) } \arguments{ \item{range}{An object of class \code{\linkS4class{GRanges}}, \code{\linkS4class{IRanges}} or a \code{data.frame} which will be coerced into one. In the former case, there should be at least the following two columns present as \code{elementMetadata}: \describe{ \item{}{\code{feature}: a factor indicating the feature type for a given track item. When plotting the track to the device and if a display parameter with the same name as the value of \code{feature} is set, this will be used as the track item's fill color. See \code{\link{grouping}} for details.} \item{}{\code{group}: a factor indicating group membership for a given track item. All items in the same group will be connected when plotting to the device. See \code{\link{grouping}} for details.} \item{}{\code{id}: a character identifier for a given track item. It's value will be used as the identifier tag when plotting to the device if the display parameter \code{showFeatureId=TRUE}.} } If \code{range} is a \code{data.frame} it needs to contain at least the columns mentioned above as well as these three additional columns: \describe{ \item{}{\code{start}, \code{end}: the start and end coordinates for the track items.} \item{}{\code{strand}: the strand information for the track items. It may be provided in the form \code{+} for the Watson strand, \code{-} for the Crick strand or \code{*} for either one of the two.} } Alternatively, the \code{range} argument may be missing, in which case the relevant information has to be provided as individual function arguments (see below). } \item{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 value will be recycled. Otherwise, the usual R recycling rules for vectors do not apply.} \item{feature}{Factor (or other vector that can be coerced into one), giving the feature types for the individual track items. Needs to be of equal length as the \code{start, end} or \code{width} vectors, or of length 1.} \item{group}{Factor (or other vector that can be coerced into one), giving the group memberships for the individual track items. Needs to be of equal length as the \code{start, end} or \code{width} vectors, or of length 1.} \item{id}{Character vector of track item identifiers. Needs to be of equal length as the \code{start, end} or \code{width} vectors, or of length 1.} \item{strand}{Character vector, the strand information for the individual track items. Needs to be of equal length as the \code{start, end} or \code{width} vectors, 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.} \item{chromosome}{The chromosome on which the track's genomic ranges are defined. A valid UCSC chromosome identifier. Please note that at this stage only syntactic checking takes place, i.e., the argument value needs to be a single integer, numeric character or a character of the form \code{chrx}, where \emph{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.} \item{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.} \item{stacking}{The stacking type for overlapping items of the track. One in \code{c(hide, dense, squish, pack,full)}. Currently, only hide (don't show the track items, squish (make best use of the available space) and dense (no stacking at all) are implemented.} \item{name}{Character scalar of the track's name used in the title panel when plotting.} \item{fun}{A function that is being called for each entry in the \code{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 \dots). These arguments are: \itemize{ \item{\code{start}: the genomic start coordinate of the range item.} \item{\code{end}: the genomic end coordinates of the range item.} \item{\code{strand}: the strand information for the range item.} \item{\code{chromosome}: the chromosome of the range item.} \item{\code{identifier}: the identifier of the range item, i.e., the result of calling \code{identifier(DetailsAnnotationTrack, lowest=TRUE)}. Typically those identifiers are passed on to the object constructor during instantiation as the \code{id} argument.} \item{\code{index}: a counter enumerating the ranges. The \code{AnnotationTrack} object is sorted internally for visibility, and the \code{index} argument refers to the index of plotting.} \item{\code{GdObject}: a reference to the currently plotted \code{DetailsAnnotationTrack} object.} \item{\code{GdObject.original}: a reference to the \code{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 \code{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 \code{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 \code{GRanges} object. } \item{selectFun}{A function that is being called for each entry in the \code{AnnotationTrack} object with exactly the same arguments as in \code{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 \code{TRUE}, details will be drawn for the item, if it is \code{FALSE}, the details strip for the item is omitted. } \item{\dots}{Additional items which will all be interpreted as further display parameters. See \code{\link{settings}} and the "Display Parameters" section below for details.} } \value{ The return value of the constructor function is a new object of class \code{AnnotationTrack} or of class \code{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. } \section{details}{ The \code{DetailsAnnotationTrack} class directly extends \code{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 \code{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 \code{DataTrack} e.g. because it requires extra space or a trellis-like representation, a \code{DetailsAnnotationTrack} can be used instead. Example: An \code{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 \code{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 \code{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 \code{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 \code{detailsFunArgs} display parameter. This is expected to be a named list, and all list elements are passed along to the plotting function \code{fun} and to the selector function \code{selectFun} as additional named arguments. Please note that some argument names like \code{start}, \code{end} or \code{identifier} are reserved and can not be used in the \code{detailsFunArgs} list. For examples of plotting functions, see the 'Examples' section. } \section{Slots}{ \describe{ \item{\code{stacking}:}{Object of class \code{"character"}, inherited from class \code{\linkS4class{StackedTrack}}} \item{\code{stacks}:}{Object of class \code{"environment"}, inherited from class \code{\linkS4class{StackedTrack}}} \item{\code{range}:}{Object of class \code{\linkS4class{GRanges}}, inherited from class \code{\linkS4class{RangeTrack}}} \item{\code{chromosome}:}{Object of class \code{"character"}, inherited from class \code{\linkS4class{RangeTrack}} } \item{\code{genome}:}{Object of class \code{"character"}, inherited from class \code{\linkS4class{RangeTrack}}} \item{\code{dp}:}{Object of class \code{\linkS4class{DisplayPars}}, inherited from class \code{\linkS4class{GdObject}} } \item{\code{name}:}{Object of class \code{"character"}, inherited from class \code{\linkS4class{GdObject}}} \item{\code{imageMap}:}{Object of class \code{\linkS4class{ImageMap}}, inherited from class \code{\linkS4class{GdObject}}} \item{\code{fun}:}{A function that is being called for each \code{AnnotationTrack} element to plot details.} \item{\code{selectFun}:}{A function that is being called for each \code{AnnotationTrack} element to decide whether details need to be plotted.} } Additional display parameters are being inherited from the \code{\linkS4class{StackedTrack}} parent class. } \section{Extends}{ Class \code{"\linkS4class{StackedTrack}"}, directly. Class \code{"\linkS4class{RangeTrack}"}, by class "StackedTrack", distance 2. Class \code{"\linkS4class{GdObject}"}, by class "StackedTrack", distance3. \code{DetailsAnnotationTrack} directly extends \code{AnnotationTrack}. } \section{Methods}{ In the following code chunks, \code{obj} is considered to be an object of class \code{AnnotationTrack} or \code{DetailsAnnotationTrack}. \bold{\emph{Exported in the name space:}} \describe{ \item{group}{\code{signature(GdObject="AnnotationTrack")}: extract the group membership for all track items. \emph{Usage:} \code{group(GdObject)} \emph{Examples:} \describe{ \item{}{\code{group(obj)}} } } \item{group<-}{\code{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. \emph{Usage:} \code{group<-(GdObject, value)} \emph{Examples:} \describe{ \item{}{\code{group(obj) <- c("a", "a", "b", "c", "a")}} } } \item{identifier}{\code{signature(GdObject="AnnotationTrack")}: return track item identifiers. Depending on the setting of the optional argument \code{lowest}, these are either the group identifiers or the individual item identifiers. \emph{Usage:} \code{identifier(GdObject, lowest=FALSE)} \emph{Additional Arguments:} \describe{ \item{}{\code{lowest}: return the lowest-level identifier, i.e., the item IDs, or the higher level group IDs which do not have to be unqiue.} } \emph{Examples:} \describe{ \item{}{\code{identifier(obj)}} \item{}{\code{identifier(obj, lowest=TRUE)}} } } \item{identifier<-}{\code{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 \code{groups<-}. \emph{Usage:} \code{identifier<-(GdObject, value)} \emph{Examples:} \describe{ \item{}{\code{identifier(obj) <- c("foo", "bar")}} } } } \bold{\emph{Internal methods:}} \describe{ \item{coerce}{\code{signature(from="AnnotationTrack", to="UCSCData")}: coerce to a \code{UCSCData} object for export to the UCSC genome browser. \emph{Examples:} \describe{ \item{}{\code{as(obj, "UCSCData")}} } } \item{collapseTrack}{\code{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 \code{\link{collapsing}} for details. \emph{Usage:} \code{collapseTrack(GdObject, diff=.pxResolution(coord="x"))} \emph{Additional Arguments:} \describe{ \item{}{\code{diff}: the minimum pixel width to display, everything below that will be inflated to a width of \code{diff}.} } \emph{Examples:} \describe{ \item{}{\code{Gviz:::collapseTrack(obj)}} } } \item{drawGD}{\code{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. \emph{Usage:} \code{drawGD(GdObject, minBase, maxBase, prepare=FALSE, subset=TRUE, ...)} \emph{Additional Arguments:} \describe{ \item{}{\code{minBase}, \code{maxBase}: the coordinate range to plot.} \item{}{\code{prepare}: run method in preparation or in production mode.} \item{}{\code{subset}: subset the object to the visible region or skip the potentially expensive subsetting operation.} \item{}{\code{\dots}: all further arguments are ignored.} } \emph{Examples:} \describe{ \item{}{\code{Gviz:::drawGD(obj)}} \item{}{\code{Gviz:::drawGD(obj, minBase=1, maxBase=100)}} \item{}{\code{Gviz:::drawGD(obj, prepare=TRUE, subset=FALSE)}} } } \item{drawGrid}{\code{signature(GdObject="AnnotationTrack")}: superpose a grid on top of a track. \emph{Usage:} \code{drawGrid(GdObject, from, to)} \emph{Additional Arguments:} \describe{ \item{}{\code{from}, \code{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.} } \emph{Examples:} \describe{ \item{}{\code{Gviz:::drawGrid(obj, from=10, to=100)}} } } \item{setStacks}{\code{signature(GdObject="AnnotationTrack")}: recompute the stacks based on the available space and on the object's track items and stacking settings. \emph{Usage:} \code{setStacks(GdObject, from, to)} \emph{Additional Arguments:} \describe{ \item{}{\code{from}, \code{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.} } \emph{Examples:} \describe{ \item{}{\code{Gviz:::setStacks(obj, from=1, to=100)}} } } \item{initialize}{\code{signature(.Object="AnnotationTrack")}: initialize the object } \item{show}{\code{signature(object="AnnotationTrack")}: show a human-readable summary of the object } } \bold{\emph{Inherited methods:}} \describe{ \item{stacking}{\code{signature(GdObject="AnnotationTrack")}: return the current stacking type. \emph{Usage:} \code{stacking(GdObject)} \emph{Examples:} \describe{ \item{}{\code{stacking(obj)}} } } \item{stacking<-}{\code{signature(GdObject="AnnotationTrack", value="character")}: set the object's stacking type to one in \code{c(hide, dense, squish, pack,full)}. \emph{Usage:} \code{stacking<-(GdObject, value)} \emph{Additional Arguments:} \describe{ \item{}{\code{value}: replacement value.} } \emph{Examples:} \describe{ \item{}{\code{stacking(obj) <- "squish" }} } } \item{stacks}{\code{signature(GdObject="AnnotationTrack")}: return the stack indices for each track item. \emph{Usage:} \code{stacks(GdObject)} \emph{Examples:} \describe{ \item{}{\code{Gviz:::stacks(obj)}} } } \item{[}{\code{signature(x="AnnotationTrack", i="ANY", j="ANY", drop="ANY")}: subset the items in the \code{AnnotationTrack} object. This is essentially similar to subsetting of the \code{\linkS4class{GRanges}} object in the \code{range} slot. For most applications, the \code{subset} method may be more appropriate. \emph{Additional Arguments:} \describe{ \item{}{\code{i}, \code{j}: subsetting indices, \code{j} is ignored.} \item{}{\code{drop}: argument is ignored.} } \emph{Examples:} \describe{ \item{}{\code{obj[1:5]}} } } \item{chromosome}{\code{signature(GdObject="AnnotationTrack")}: return the chromosome for which the track is defined. \emph{Usage:} \code{chromosome(GdObject)} \emph{Examples:} \describe{ \item{}{\code{chromosome(obj)}} } } \item{chromosome<-}{\code{signature(GdObject="AnnotationTrack")}: 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. \emph{Usage:} \code{chromosome<-(GdObject, value)} \emph{Additional Arguments:} \describe{ \item{}{\code{value}: replacement value.} } \emph{Examples:} \describe{ \item{}{\code{chromosome(obj) <- "chr12"}} } } \item{start, end, width}{\code{signature(x="AnnotationTrack")}: the start or end coordinates of the track items, or their width in genomic coordinates. \emph{Usage:} \code{start(x)} \code{end(x)} \code{width(x)} \emph{Examples:} \describe{ \item{}{\code{start(obj)}} \item{}{\code{end(obj)}} \item{}{\code{width(obj)}} } } \item{start<-, end<-, width<-}{\code{signature(x="AnnotationTrack")}: replace the start or end coordinates of the track items, or their width. \emph{Usage:} \code{start<-(x, value)} \code{end<-(x, value)} \code{width<-(x, value)} \emph{Additional Arguments:} \describe{ \item{}{\code{value}: replacement value.} } \emph{Examples:} \describe{ \item{}{\code{start(obj) <- 1:10}} \item{}{\code{end(obj) <- 20:30}} \item{}{\code{width(obj) <- 1}} } } \item{position}{\code{signature(GdObject="AnnotationTrack")}: the arithmetic mean of the track item's coordionates, i.e., \code{(end(obj)-start(obj))/2}. \emph{Usage:} \code{position(GdObject)} \emph{Examples:} \describe{ \item{}{\code{position(obj)}} } } \item{feature}{\code{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 \code{\link{grouping}} for details. \emph{Usage:} \code{feature(GdObject)} \emph{Examples:} \describe{ \item{}{\code{feature(obj)}} } } \item{feature<-}{\code{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 \code{AnnotationTrack}. See \code{\link{grouping}} for details. \emph{Usage:} \code{feature<-(GdObject, value)} \emph{Additional Arguments:} \describe{ \item{}{\code{value}: replacement value.} } \emph{Examples:} \describe{ \item{}{\code{feature(obj) <- c("a", "a", "b", "c", "a")}} } } \item{genome}{\code{signature(x="AnnotationTrack")}: return the track's genome. \emph{Usage:} \code{genome(x)} \emph{Examples:} \describe{ \item{}{\code{genome(obj)}} } } \item{genome<-}{\code{signature(x="AnnotationTrack")}: set the track's genome. Usually this has to be a valid UCSC identifier, however this is not formally enforced here. \emph{Usage:} \code{genome<-(x, value)} \emph{Additional Arguments:} \describe{ \item{}{\code{value}: replacement value.} } \emph{Examples:} \describe{ \item{}{\code{genome(obj) <- "mm9"}} } } \item{length}{\code{signature(x="AnnotationTrack")}: return the number of items in the track. \emph{Usage:} \code{length(x)} \emph{Examples:} \describe{ \item{}{\code{length(obj)}} } } \item{range}{\code{signature(x="AnnotationTrack")}: return the genomic coordinates for the track as an object of class \code{\linkS4class{IRanges}}. \emph{Usage:} \code{range(x)} \emph{Examples:} \describe{ \item{}{\code{range(obj)}} } } \item{ranges}{\code{signature(x="AnnotationTrack")}: return the genomic coordinates for the track along with all additional annotation information as an object of class \code{\linkS4class{GRanges}}. \emph{Usage:} \code{ranges(x)} \emph{Examples:} \describe{ \item{}{\code{ranges(obj)}} } } \item{split}{\code{signature(x="AnnotationTrack")}: split a \code{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 \code{AnnotationTrack}. \emph{Usage:} \code{split(x, f, ...)} \emph{Additional Arguments:} \describe{ \item{}{\code{f}: the splitting factor.} \item{}{\code{\dots}: all further arguments are ignored.} } \emph{Examples:} \describe{ \item{}{\code{split(obj, c("a", "a", "b", "c", "a"))}} } } \item{strand}{\code{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. \emph{Usage:} \code{strand(x)} \emph{Examples:} \describe{ \item{}{\code{strand(obj)}} } } \item{strand<-}{\code{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. \emph{Usage:} \code{strand<-(x, value)} \emph{Additional Arguments:} \describe{ \item{}{\code{value}: replacement value.} } \emph{Examples:} \describe{ \item{}{\code{strand(obj) <- "+"}} } } \item{values}{\code{signature(x="AnnotationTrack")}: return all additional annotation information except for the genomic coordinates for the track items as a data.frame. \emph{Usage:} \code{values(x)} \emph{Examples:} \describe{ \item{}{\code{values(obj)}} } } \item{coerce}{\code{signature(from="AnnotationTrack", to="data.frame")}: coerce the \code{\linkS4class{GRanges}} object in the \code{range} slot into a regular data.frame. \emph{Examples:} \describe{ \item{}{\code{as(obj, "data.frame")}} } } \item{subset}{\code{signature(x="AnnotationTrack")}: subset a \code{AnnotationTrack} by coordinates and sort if necessary. \emph{Usage:} \code{subset(x, from, to, sort=FALSE, ...)} \emph{Additional Arguments:} \describe{ \item{}{\code{from}, \code{to}: the coordinates range to subset to.} \item{}{\code{sort}: sort the object after subsetting. Usually not necessary.} \item{}{\code{\dots}: additional arguments are ignored.} } \emph{Examples:} \describe{ \item{}{\code{subset(obj, from=10, to=20, sort=TRUE)}} } } \item{displayPars}{\code{signature(x="AnnotationTrack", name="character")}: list the value of the display parameter \code{name}. See \code{\link{settings}} for details on display parameters and customization. \emph{Usage:} \code{displayPars(x, name)} \emph{Examples:} \describe{ \item{}{\code{displayPars(obj, "col")}} } } \item{displayPars}{\code{signature(x="AnnotationTrack", name="missing")}: list the value of all available display parameters. See \code{\link{settings}} for details on display parameters and customization. \emph{Examples:} \describe{ \item{}{\code{displayPars(obj)}} } } \item{getPar}{\code{signature(x="AnnotationTrack", name="character")}: alias for the \code{displayPars} method. See \code{\link{settings}} for details on display parameters and customization. \emph{Usage:} \code{getPar(x, name)} \emph{Examples:} \describe{ \item{}{\code{getPar(obj, "col")}} } } \item{getPar}{\code{signature(x="AnnotationTrack", name="missing")}: alias for the \code{displayPars} method. See \code{\link{settings}} for details on display parameters and customization. \emph{Examples:} \describe{ \item{}{\code{getPar(obj)}} } } \item{displayPars<-}{\code{signature(x="AnnotationTrack", value="list")}: set display parameters using the values of the named list in \code{value}. See \code{\link{settings}} for details on display parameters and customization. \emph{Usage:} \code{displayPars<-(x, value)} \emph{Examples:} \describe{ \item{}{\code{displayPars(obj) <- list(col="red", lwd=2)}} } } \item{setPar}{\code{signature(x="AnnotationTrack", value="character")}: set the single display parameter \code{name} to \code{value}. Note that display parameters in the \code{AnnotationTrack} class are pass-by-reference, so no re-assignmnet to the symbol \code{obj} is necessary. See \code{\link{settings}} for details on display parameters and customization. \emph{Usage:} \code{setPar(x, name, value)} \emph{Additional Arguments:} \describe{ \item{}{\code{name}: the name of the display parameter to set.} } \emph{Examples:} \describe{ \item{}{\code{setPar(obj, "col", "red")}} } } \item{setPar}{\code{signature(x="AnnotationTrack", value="list")}: set display parameters by the values of the named list in \code{value}. Note that display parameters in the \code{AnnotationTrack} class are pass-by-reference, so no re-assignmnet to the symbol \code{obj} is necessary. See \code{\link{settings}} for details on display parameters and customization. \emph{Examples:} \describe{ \item{}{\code{setPar(obj, list(col="red", lwd=2))}} } } \item{names}{\code{signature(x="AnnotationTrack")}: return the value of the \code{name} slot. \emph{Usage:} \code{names(x)} \emph{Examples:} \describe{ \item{}{\code{names(obj)}} } } \item{names<-}{\code{signature(x="AnnotationTrack", value="character")}: set the value of the \code{name} slot. \emph{Usage:} \code{names<-(x, value)} \emph{Examples:} \describe{ \item{}{\code{names(obj) <- "foo"}} } } \item{coords}{\code{signature(ImageMap="AnnotationTrack")}: return the coordinates from the internal image map. \emph{Usage:} \code{coords(ImageMap)} \emph{Examples:} \describe{ \item{}{\code{coords(obj)}} } } \item{tags}{\code{signature(x="AnnotationTrack")}: return the tags from the internal image map. \emph{Usage:} \code{tags(x)} \emph{Examples:} \describe{ \item{}{\code{tags(obj)}} } } } } \section{Display Parameters}{ The following display parameters are set for objects of class \code{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 \code{\link{settings}} for details on setting graphical parameters for tracks. \describe{ \item{}{\code{cex=1}: Numeric scalar. The font expansion factor for item identifiers.} \item{}{\code{cex.group=0.6}: Numeric scalar. The font expansion factor for the group-level annotation.} \item{}{\code{col="transparent"}: Character or integer scalar. The border color for all track items.} \item{}{\code{fill="lightblue"}: Character or integer scalar. The fill color for untyped items. This is also used to connect grouped items. See \code{\link{grouping}} for details.} \item{}{\code{fontcolor="white"}: Character or integer scalar. The font color for item identifiers.} \item{}{\code{fontcolor.group="#808080"}: Character or integer scalar. The font color for the group-level annotation.} \item{}{\code{fontface=1}: Integer scalar. The font face for item identifiers.} \item{}{\code{fontface.group=2}: Numeric scalar. The font face for the group-level annotation.} \item{}{\code{fontfamily="sans"}: Character scalar. The font family for item identifiers.} \item{}{\code{fontsize=12}: Numeric scalar. The font size for item identifiers.} \item{}{\code{lex=1}: Numeric scalar. The line expansion factor for all track items. This is also used to connect grouped items. See \code{\link{grouping}} for details.} \item{}{\code{lineheight=1}: Numeric scalar. The font line height for item identifiers.} \item{}{\code{lty="solid"}: Character or integer scalar. The line type for all track items. This is also used to connect grouped items. See \code{\link{grouping}} for details.} \item{}{\code{lwd=1}: Integer scalar. The line width for all track items. This is also used to connect grouped items. See \code{\link{grouping}} for details.} \item{}{\code{rotation=0}: Numeric scalar. The degree of text rotation for item identifiers.} \item{}{\code{shape="arrow"}: Character scalar. The shape in which to display the track items. Currently only \code{box}, \code{arrow}, \code{ellipse}, and \code{smallArrow} are implemented.} \item{}{\code{showFeatureId=FALSE}: Logical scalar. Control whether to plot the individual track item identifiers.} \item{}{\code{showId=FALSE}: Logical scalar. Control whether to annotate individual groups.} \item{}{\code{showOverplotting=FALSE}: Logical scalar. Use a color gradient to show the amount of overplotting for collapsed items. This implies that \code{collapse==TRUE}} \item{}{\code{size=1}: Numeric scalar. The relative size of the track. Can be overridden in the \code{\link{plotTracks}} function.} \item{}{\code{mergeGroups=FALSE}: Logical scalar. Merge fully overlapping groups if \code{collapse==TRUE}.} } \code{DetailsAnnotationTrack} adds the following additional display parameters: \describe{ \item{}{\code{details.size=0.5}: Numeric scalar. The fraction of vertical space of the track used for the details section.} \item{}{\code{details.minWidth=100}: Numeric scalar. The minium width in pixels for a details panel, if less space is available no details are plotted.} \item{}{\code{detailsConnector.col="darkgray"}: Character or integer scalar. Color of the line connecting the \code{AnnotstionTrack} item with its details panel.} \item{}{\code{detailsConnector.lty="dashed"}: Character or integer scalar. Type of connecting line.} \item{}{\code{detailsConnector.lwd=1}: Integer scalar. Line width of the connector.} \item{}{\code{detailsConnector.pch=20}: Integer scalar. Type of the connector's ends.} \item{}{\code{detailsConnector.cex=1}: Numeric scalar. Relative size of the connector's end points.} \item{}{\code{detailsBorder.lty="solid"}: Character or integer scalar. Line type of the border around each details panel.} \item{}{\code{detailsBorder.lwd=1}: Integer scalar. Line width of the border.} \item{}{\code{detailsBorder.col="darkgray"}: Character or integer scalar. Line color of the border.} \item{}{\code{detailsBorder.fill="transparent"}: Character or integer scalar. Background color of the border.} \item{}{\code{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 \code{size} and \code{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.} \item{}{\code{detailsFunArgs=list()}: List. Additional arguments that get passed on the the details plotting function.} \item{}{\code{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 \code{AnnotationTrack} \code{DetailsAnnotationTrack} objects. \describe{ \item{}{\code{\linkS4class{GdObject}}: \describe{ \item{}{\code{alpha=1}: Numeric scalar. The transparency for all track items.} \item{}{\code{background.panel="transparent"}: Integer or character scalar. The background color of the content panel.} \item{}{\code{background.title="lightgray"}: Integer or character scalar. The background color for the title panels.} \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion factor for the axis annotation. Defaults to \code{NULL}, in which case it is computed based on the available space.} \item{}{\code{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 \code{NULL}, which means that the text size is automatically adjusted to the available space.} \item{}{\code{col.axis="white"}: Integer or character scalar. The font and line color for the y axis, if any.} \item{}{\code{col.frame="lightgray"}: Integer or character scalar. The line color used for the panel frame, if \code{frame==TRUE}} \item{}{\code{col.grid="#808080"}: Integer or character scalar. Default line color for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{col.line=NULL}: Integer or character scalar. Default colors for plot lines. Usually the same as the global \code{col} parameter.} \item{}{\code{col.symbol=NULL}: Integer or character scalar. Default colors for plot symbols. Usually the same as the global \code{col} parameter.} \item{}{\code{col.title="white"}: Integer or character scalar. The font color for the title panels.} \item{}{\code{collapse=TRUE}: Boolean controlling wether to collapse the content of the track to accomodate the minimum current device resolution. See \code{\link{collapsing}} for details.} \item{}{\code{fontface.title=2}: Integer or character scalar. The font face for the title panels.} \item{}{\code{fontfamily.title="sans"}: Integer or character scalar. The font family for the title panels.} \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the track when plotting.} \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting of a grid.} \item{}{\code{h=-1}: Integer scalar. Parameter controlling the number of horizontal grid lines, see \code{\link{panel.grid}} for details.} \item{}{\code{lty.grid="solid"}: Integer or character scalar. Default line type for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{min.distance=1}: Numeric scalar. The minimum pixel distance before collapsing range items, only if \code{collapse==TRUE}. See \code{\link{collapsing}} for details.} \item{}{\code{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 \code{\link{collapsing}} for details.} \item{}{\code{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 \code{\link{collapsing}} for details.} \item{}{\code{showAxis=TRUE}: Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).} \item{}{\code{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 \code{\link{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.} \item{}{\code{v=-1}: Integer scalar. Parameter controlling the number of vertical grid lines, see \code{\link{panel.grid}} for details.} } } } } \author{Florian Hahne, Arne Mueller} \seealso{ \code{\linkS4class{DisplayPars}} \code{\linkS4class{GdObject}} \code{\linkS4class{GRanges}} \code{\linkS4class{ImageMap}} \code{\linkS4class{IRanges}} \code{\linkS4class{RangeTrack}} \code{\linkS4class{StackedTrack}} \code{\link{collapsing}} \code{\link{DataTrack}} \code{\link{grouping}} \code{\link{panel.grid}} \code{\link{plotTracks}} \code{\link{settings}} } \examples{ ## 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 <- GenomicRanges::GRanges(seqnames="chr7", range=IRanges::IRanges(start=df$start, end=df$end), strand=str) IRanges::elementMetadata(gr) <- df[,-(1:3)] annTrack <- AnnotationTrack(range=gr, genome="hg19", chromosome=7, name="generic annotation", stacking="squish") \dontshow{ ## For some annoying reason the postscript device does not know about ## the sans font if(!interactive()) { font <- ps.options()$family displayPars(annTrack) <- list(fontfamily=font, fontfamily.title=font) } } ## Plotting plotTracks(annTrack) ## Track names names(annTrack) names(annTrack) <- "foo" plotTracks(annTrack) ## Subsetting and splitting subTrack <- subset(annTrack, to=2155000) length(subTrack) subTrack[1:2] split(annTrack, c(1,2,1,2)) ## Accessors start(annTrack) end(annTrack) width(annTrack) position(annTrack) width(subTrack) <- width(subTrack)+1000 strand(annTrack) strand(subTrack) <- "-" chromosome(annTrack) chromosome(subTrack) <- "chrX" genome(annTrack) genome(subTrack) <- "mm9" range(annTrack) ranges(annTrack) ## Annotation identifier(annTrack) identifier(annTrack, lowest=TRUE) identifier(subTrack) <- "bar" feature(annTrack) feature(subTrack) <- "foo" values(annTrack) ## Grouping group(annTrack) group(subTrack) <- "Group 1" chromosome(subTrack) <- "chr7" plotTracks(subTrack) ## Stacking stacking(annTrack) stacking(annTrack) <- "dense" plotTracks(annTrack) ## coercion as(annTrack, "data.frame") as(annTrack, "UCSCData") ## HTML image map coords(annTrack) tags(annTrack) annTrack <- plotTracks(annTrack)$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=TRUE) ## 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) } \keyword{classes}