\name{GeneRegionTrack-class} \Rdversion{1.1} \docType{class} \alias{GeneRegionTrack-class} \alias{GeneRegionTrack} \alias{coerce,GeneRegionTrack,UCSCData-method} \alias{collapseTrack,GeneRegionTrack-method} \alias{exon} \alias{exon,GeneRegionTrack-method} \alias{exon<-} \alias{exon<-,GeneRegionTrack,character-method} \alias{gene,GeneRegionTrack-method} \alias{gene} \alias{gene<-,GeneRegionTrack,character-method} \alias{gene<-} \alias{group,GeneRegionTrack-method} \alias{group<-,GeneRegionTrack,character-method} \alias{identifier,GeneRegionTrack-method} \alias{identifier<-,GeneRegionTrack,character-method} \alias{initialize,GeneRegionTrack-method} \alias{show,GeneRegionTrack-method} \alias{symbol,GeneRegionTrack-method} \alias{symbol<-,GeneRegionTrack,character-method} \alias{symbol} \alias{symbol<-} \alias{transcript,GeneRegionTrack-method} \alias{transcript<-,GeneRegionTrack,character-method} \alias{transcript} \alias{transcript<-} \title{GeneRegionTrack class and methods} \description{ A class to hold gene model data for a genomic region. } \section{Objects from the class}{ Objects can be created using the constructor function \code{GeneRegionTrack}. } \usage{ GeneRegionTrack(range=NULL, rstarts=NULL, rends=NULL, rwidths=NULL, strand="*", feature="unknown", exon=feature, transcript=feature, gene=feature, symbol=feature, chromosome, genome, stacking="squish", name="GeneRegionTrack", start, end, ...) } \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 may be one or more of the following 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{gene}: a factor for the gene identifier of a given track item..} \item{}{\code{transcript}: a factor for the transcript identifier of a given track item. All items with the same transcript identifier will be connected when plotting to the device. See \code{\link{grouping}} for details. Will be used as labels when \code{showId=TRUE}, and \code{geneSymbol=FALSE}.} \item{}{\code{exon}: a factor with the exon 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{showExonId=TRUE}.} \item{}{\code{symbol}: a factor with human-readable gene name aliases which will be used as labels when \code{showId=TRUE}, and \code{geneSymbol=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}{An integer scalar with the genomic start coordinates for the gene model range. If this is missing, the default value will automatically be the smallest value in \code{rstarts}.} \item{end}{An integer scalar with the genomic end coordinates for the gene model range. If this is missing, the default value will automatically be the largest value in \code{rends}.} \item{rstarts}{An integer vector of the start coordinates for the actual gene model items, i.e., for the individual exons. The relationship between exons is handled via the \code{gene} and \code{transcript} factors. Alternatively, this can be a vector of comma-separated lists of integer coordinates, one vector item for each transcript, and each comma-separated element being the start location of a single exon within that transcript. Those lists will be exploded upon object instantiation and all other annotation arguments will be recycled accordingly to regenerate the exon/transcript/gene relationship structure. This implies the approriate number of items in all annotation and coordinates arguments.} \item{rends}{An integer vector of the end coordinates for the actual gene model items. Both \code{rstarts} and \code{rends} have to be of equal length.} \item{rwidths}{An integer vector of widths for the actual gene model items. This can be used instead of either \code{rstarts} or \code{rends} to specify the range coordinates.} \item{feature}{Factor (or other vector that can be coerced into one), giving the feature types for the individual track exons.} \item{exon}{Character vector of exon identifiers.} \item{strand}{Character vector, the strand information for the individual track exons. Please note that all items within a single gene or transcript model need to be on the same strand, and erroneous entries will result in casting of an error.} \item{transcript}{Factor (or other vector that can be coerced into one), giving the transcript memberships for the individual track exons.} \item{gene}{Factor (or other vector that can be coerced into one), giving the gene memberships for the individual track exons.} \item{symbol}{Factor (or other vector that can be coerced into one), giving the associated gene symbols for the individual track exons.} \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 arguments value needs to be a single integer, numeric character or a character of the form \code{chrx}, where \code{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{\dots}{Additional items which will all be interpreted as further display parameters. See \code{\link{settings}} and the "Display Parameters" section below for details.} } \details{ A track containing all gene models in a particular region. The data are usually fetched dynamially from an online data store, but it is also possible to manully construct objects from local data. Particular data sources should be implemented as sub-classes, and \code{GeneRegionTrack} is just the commone denominator that is being used for plotting later on. There are several levels of data associated to a \code{GeneRegionTrack}: \describe{ \item{exon level:}{identifiers are stored in the exon column of the \code{\linkS4class{GRanges}} object in the \code{range} slot. Data may be extracted using the \code{exon} method.} \item{transcript level:}{identifiers are stored in the transcript column of the \code{\linkS4class{GRanges}} object. Data may be extracted using the \code{transcript} method.} \item{gene level:}{identifiers are stored in the gene column of the \code{\linkS4class{GRanges}} object, more human-readable versions in the symbol column. Data may be extracted using the \code{gene} or the \code{symbol} methods.} \item{transcript-type level:}{information is stored in the feature column of the \code{\linkS4class{GRanges}} object. If a display parameter of the same name is specified, the software will use its value for the coloring.} } } \value{ The return value of the constructor function is a new object of class \code{GeneRegionTrack}. } \section{Slots}{ \describe{ \item{\code{start}:}{Object of class \code{"numeric"}, the start coordinates of the annotation range. The coorrdinates for the individual gene model items are stored in the \code{range} slot.} \item{\code{end}:}{Object of class \code{"numeric"}, the end coordinates of the annotation range. The corrdinates for the individual gene model items are stored in the \code{range} slot. } \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}}} } } \section{Extends}{ Class \code{"\linkS4class{AnnotationTrack}"}, directly. Class \code{"\linkS4class{StackedTrack}"}, by class "AnnotationTrack", distance2. Class \code{"\linkS4class{RangeTrack}"}, by class "AnnotationTrack", distance3. Class \code{"\linkS4class{GdObject}"}, by class "AnnotationTrack", distance4. } \section{Methods}{ In the following code chunks, \code{obj} is considered to be an object of class \code{GeneRegionTrack}. \bold{\emph{Exported in the name space:}} \describe{ \item{group}{\code{signature(gdObject="GeneRegionTrack")}: 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="GeneRegionTrack", 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="GeneRegionTrack")}: 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, lowest=FALSE)}} } } \item{identifier<-}{\code{signature(gdObject="GeneRegionTrack", 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")}} } } \item{exon}{\code{signature(GdObject="GeneRegionTrack")}: Extract the exon identifiers for all exons in the gene models. \emph{Usage:} \code{exon(GdObject)} \emph{Examples:} \describe{ \item{}{\code{exon(obj)}} } } \item{exon<-}{\code{signature(GdObject="GeneRegionTrack", value="character")}: replace the exon identifiers for all exons in the gene model. The replacement value must be a character of appropriate length or another vector that can be coerced into such. \emph{Usage:} \code{exon<-(GdObject, value)} \emph{Examples:} \describe{ \item{}{\code{exon(obj) <- paste("Exon", 1:5)}} } } \item{gene}{\code{signature(GdObject="GeneRegionTrack")}: Extract the gene identifiers for all gene models. \emph{Usage:} \code{gene(GdObject)} \emph{Examples:} \describe{ \item{}{\code{gene(obj)}} } } \item{gene<-}{\code{signature(GdObject="GeneRegionTrack", value="character")}: replace the gene identifiers for all gene models. The replacement value must be a character of appropriate length or another vector that can be coerced into such. \emph{Usage:} \code{gene<-(GdObject, value)} \emph{Examples:} \describe{ \item{}{\code{gene(obj) <- paste("Gene", LETTERS[1:5])}} } } \item{symbol}{\code{signature(GdObject="GeneRegionTrack")}: Extract the human-readble gene symbol for all gene models. \emph{Usage:} \code{symbol(GdObject)} \emph{Examples:} \describe{ \item{}{\code{symbol(obj)}} } } \item{symbol<-}{\code{signature(GdObject="GeneRegionTrack", value="character")}: replace the human-readable gene symbol for all gene models. The replacement value must be a character of appropriate length or another vector that can be coerced into such. \emph{Usage:} \code{gene<-(GdObject, value)} \emph{Examples:} \describe{ \item{}{\code{symbol(obj) <- letters[1:5]}} } } \item{transcript}{\code{signature(GdObject="GeneRegionTrack")}: Extract the transcript identifiers for all transcripts in the gene models. \emph{Usage:} \code{transcript(GdObject)} \emph{Examples:} \describe{ \item{}{\code{transcript(obj)}} } } \item{transcript<-}{\code{signature(GdObject="GeneRegionTrack", value="character")}: replace the transcript identifiers for all transcripts in the gene model. The replacement value must be a character of appropriate length or another vector that can be coerced into such. \emph{Usage:} \code{transcript<-(GdObject, value)} \emph{Examples:} \describe{ \item{}{\code{transcript(obj) <- paste("Exon", 1:5)}} } } } \emph{Internal methods:} \describe{ \item{coerce}{\code{signature(from="GeneRegionTrack", 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="GeneRegionTrack")}: 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{initialize}{\code{signature(.Object="GeneRegionTrack")}: initialize the object } \item{show}{\code{signature(object="GeneRegionTrack")}: show a human-readable summary of the object } } \bold{\emph{Inherited methods:}} \describe{ \item{drawGD}{\code{signature(GdObject="GeneRegionTrack")}: 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="GeneRegionTrack")}: 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="GeneRegionTrack")}: 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{stacking}{\code{signature(GdObject="GeneRegionTrack")}: return the current stacking type. \emph{Usage:} \code{stacking(GdObject)} \emph{Examples:} \describe{ \item{}{\code{stacking(obj)}} } } \item{stacking<-}{\code{signature(GdObject="GeneRegionTrack", 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="GeneRegionTrack")}: 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="GeneRegionTrack", i="ANY", j="ANY", drop="ANY")}: subset the items in the \code{GeneRegionTrack} 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="GeneRegionTrack")}: 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="GeneRegionTrack")}: 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="GeneRegionTrack")}: 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="GeneRegionTrack")}: 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="GeneRegionTrack")}: 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="GeneRegionTrack")}: 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="GeneRegionTrack", 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{GeneRegionTrack}. 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="GeneRegionTrack")}: return the track's genome. \emph{Usage:} \code{genome(x)} \emph{Examples:} \describe{ \item{}{\code{genome(obj)}} } } \item{genome<-}{\code{signature(x="GeneRegionTrack")}: 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="GeneRegionTrack")}: 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="GeneRegionTrack")}: 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="GeneRegionTrack")}: 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="GeneRegionTrack")}: split a \code{GeneRegionTrack} 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{GeneRegionTrack}. \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="GeneRegionTrack")}: 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="GeneRegionTrack")}: 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="GeneRegionTrack")}: 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="GeneRegionTrack", 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="GeneRegionTrack")}: subset a \code{GeneRegionTrack} 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="GeneRegionTrack", 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="GeneRegionTrack", 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="GeneRegionTrack", 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="GeneRegionTrack", 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="GeneRegionTrack", 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="GeneRegionTrack", value="character")}: set the single display parameter \code{name} to \code{value}. Note that display parameters in the \code{GeneRegionTrack} 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="GeneRegionTrack", value="list")}: set display parameters by the values of the named list in \code{value}. Note that display parameters in the \code{GeneRegionTrack} 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="GeneRegionTrack")}: 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="GeneRegionTrack", 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="GeneRegionTrack")}: 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="GeneRegionTrack")}: 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{GeneRegionTrack} 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{fill="orange"}: 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{geneSymbols=TRUE}: Logical scalar. Use human-readable gene symbols or gene IDs for the transcript annotation.} \item{}{\code{shape=c("smallArrow", "box")}: 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{showExonId=FALSE}: Logical scalar. Control whether to plot the individual exon identifiers.} \item{}{\code{collapseTranscripts=FALSE}: Logical scalar. Merge all transcripts of the same gene into one single gene model. Essentially, this will only keep the start location of the first exon and the end location of the last exon from all transcripts of a gene.} } 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{GeneRegionTrack} objects. \describe{ \item{}{\code{\linkS4class{AnnotationTrack}}: \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{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{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}.} } } \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} \seealso{ \code{\linkS4class{AnnotationTrack}} \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{ ## Load some sample data data(cyp2b10) ## Construct the object grTrack <- GeneRegionTrack(start=26682683, end=26711643, rstart=cyp2b10$start, rends=cyp2b10$end, chromosome=7, genome="mm9", transcript=cyp2b10$transcript, gene=cyp2b10$gene, symbol=cyp2b10$symbol, name="Cyp2b10", strand=cyp2b10$strand) \dontshow{ ## For some annoying reason the postscript device does not know about ## the sans font if(!interactive()) { font <- ps.options()$family displayPars(grTrack) <- list(fontfamily=font, fontfamily.title=font) } } ## Plotting plotTracks(grTrack) ## Track names names(grTrack) names(grTrack) <- "foo" plotTracks(grTrack) ## Subsetting and splitting subTrack <- subset(grTrack, from=26700000, to=26705000) length(subTrack) subTrack <- grTrack[transcript(grTrack)=="ENSMUST00000144140"] split(grTrack, transcript(grTrack)) ## Accessors start(grTrack) end(grTrack) width(grTrack) position(grTrack) width(subTrack) <- width(subTrack)+100 strand(grTrack) strand(subTrack) <- "-" chromosome(grTrack) chromosome(subTrack) <- "chrX" genome(grTrack) genome(subTrack) <- "hg19" range(grTrack) ranges(grTrack) ## Annotation identifier(grTrack) identifier(grTrack, lowest=TRUE) identifier(subTrack) <- "bar" feature(grTrack) feature(subTrack) <- "foo" exon(grTrack) exon(subTrack) <- letters[1:2] gene(grTrack) gene(subTrack) <- "bar" symbol(grTrack) symbol(subTrack) <- "foo" transcript(grTrack) transcript(subTrack) <- c("foo", "bar") chromosome(subTrack) <- "chr7" plotTracks(subTrack) values(grTrack) ## Grouping group(grTrack) group(subTrack) <- "Group 1" transcript(subTrack) plotTracks(subTrack) ## Stacking stacking(grTrack) stacking(grTrack) <- "dense" plotTracks(grTrack) ## coercion as(grTrack, "data.frame") as(grTrack, "UCSCData") ## HTML image map coords(grTrack) tags(grTrack) grTrack <- plotTracks(grTrack)$foo coords(grTrack) tags(grTrack) } \keyword{classes}