R/settings.R

In ivanek/Gviz: Plotting data and annotation information along genomic coordinates

#' Setting display parameters to control the look and feel of the plots
#'
#'
#' The genome track plots in this package are all highly customizable by means
#' of so called 'display parameters'. This page highlights the use of these
#' parameters and list all available settings for the different track classes.
#'
#'
#' All of the package's track objects inherit the \code{dp} slot from the
#' \code{\linkS4class{GdObject}} parent class, which is the main container to
#' store an object's display parameters. Internally, the content of this slot
#' has to be an object of class \code{\linkS4class{DisplayPars}}, but the user
#' is usually not exposed to this low level implementation. Instead, there are
#' two main interaction points, namely the individual object constructor
#' functions and the final \code{\link{plotTracks}} function. In both cases,
#' all additional arguments that are not caught by any of the formally defined
#' function parameters are being interpreted as additional display parameters
#' and are automatically added to the aforementioned slot. The main difference
#' here is that display parameters that are passed on to the constructor
#' function are specific for an individual track object, whereas those supplied
#' to the \code{plotTracks} function will be applied to all the objects in the
#' plotting list. Not all display parameters have an effect on the plotting of
#' all track classes, and those will be silently ignored.
#'
#' One can query the available display parameters for a given class as well as
#' their default values by calling the \code{\link{availableDisplayPars}}
#' function, or by inspecting the man pages of the individual track classes.
#' The structure of the classes defined in this package is hierarchical, and so
#' are the available display parameters, i.e., all objects inherit the
#' parameters defined in the commom \code{GdObject} parent class, and so on.
#'
#' Once a track object has been created, the display parameters are still open
#' for modification. To this end, the \code{\linkS4class{DisplayPars}} replacement
#' method is available for all objects inheriting from class \code{GdObject}.
#' The method takes a named list of parameters as input, e.g.:
#'
#' \code{displayPars(foo) <- list(col="red", lwd=2)}
#'
#' In the same spirit, the currently set display parameters for the object
#' \code{foo} can be inferred using the \code{displayPars} method directly,
#' e.g.:
#'
#' \code{displayPars(foo)}
#'
#' For track objects inheriting from class
#' \code{\linkS4class{AnnotationTrack}}, display parameters that are not
#' formally defined in the class definition or in any of the parent classes are
#' considered to be valid R color identifiers that are used to distinguish
#' between different types of annotation features. For instance, the parameter
#' 'miRNA' will be used to color all annotation features of class miRNA. The
#' annotation types can be set in the constructor function of the track object
#' via the \code{feature} argument. For most of the tracks that have been
#' inferred from one of the online repositories, this classification will
#' usually be downloaded along with the actual annotation data.
#'
#' Users might find themselves changing the same parameters over and over
#' again, and it would make sense to register these modifications in a central
#' location once and for all. To this end the Gviz package supports display
#' parameter schemes. A scheme is essentially just a bunch of nested named
#' lists, where the names on the first level of nesting should correspond to
#' track class names, and the names on the second level to the display
#' parameters to set. The currently active schmeme can be changed by setting
#' the global option \code{Gviz.scheme}, and a new scheme can be registered by
#' using the \code{addScheme} function, providing both the list and the name
#' for the new scheme. The \code{getScheme} function is useful to get the
#' current scheme as a list structure, for instance to use as a skeleton for
#' your own custom scheme.
#'
#' In order to make these settings persitant across R sessions one can create
#' one or several schemes in the global environment in the special object
#' \code{.GvizSchemes}, for instance by putting the necessary code in the
#' \code{.Rprofile} file. This object needs to be a named list of schemes, and
#' it will be collected when the Givz package loads. Its content is then
#' automatically added to the collection of available schemes.
#'
#' Please note that because display parameters are stored with the track
#' objects, a scheme change only has an effect on those objects that are
#' created after the change has taken place.
#'
#' @aliases settings addScheme getScheme
#' @param scheme A named nested list of display parameters, where the first
#' level of nesting represents Gviz track object classes, and the second level
#' of nesting represents parameters.
#' @param name A character scalar with the scheme name.
#' @return
#'
#' The \code{getScheme} function returns current scheme as a list structure.
#' @section Display Parameters:
#'
#' \describe{
#'
#' \item{GenomeAxisTrack:}{
#'
#' \describe{
#'
#' \item{\code{add35=FALSE}:}{ Logical scalar. Add 3' to 5' direction
#' indicators.}
#'
#' \item{\code{add53=FALSE}:}{ Logical scalar. Add 5' to 3' direction
#' indicators.}
#'
#' \item{\code{background.title="transparent"}:}{ Character scalar.  The
#' background color for the title panel. Defaults to omit the background.}
#'
#' \item{\code{cex.id=0.7}:}{ Numeric scalar. The text size for the optional
#' range annotation.}
#'
#' \item{\code{cex=0.8}:}{ Numeric scalar. The overall font expansion factor
#' for the axis annotation text.}
#'
#' \item{\code{col.border.title="transparent"}:}{ Integer or character scalar.
#' The border color for the title panels.}
#'
#' \item{\code{lwd.border.title=1}:}{ Integer scalar. The border width for the
#' title panels.}
#'
#' \item{\code{col.id="white"}:}{ Character scalar. The text color for the
#' optional range annotation.}
#'
#' \item{\code{col.range="cornsilk4"}:}{ Character scalar. The border color for
#' highlighted regions on the axis.}
#'
#' \item{\code{distFromAxis=1}:}{ Numeric scalar. Control the distance of the
#' axis annotation from the tick marks.}
#'
#' \item{\code{exponent=NULL}:}{ Numeric scalar. The exponent for the axis
#' coordinates, e.g., 3 means mb, 6 means gb, etc. The default is to
#' automatically determine the optimal exponent.}
#'
#' \item{\code{fill.range="cornsilk3"}:}{ Character scalar. The fill color for
#' highlighted regions on the axis.}
#'
#' \item{\code{fontcolor="#808080"}:}{ Character scalar. The font color for the
#' axis annotation text.}
#'
#' \item{\code{fontsize=10}:}{ Numeric scalar. Font size for the axis
#' annotation text in points.}
#'
#' \item{\code{labelPos="alternating"}:}{ Character vector, one in
#' "alternating", "revAlternating", "above" or "below". The vertical
#' positioning of the axis labels. If \code{scale} is not \code{NULL}, the
#' possible values are "above", "below" and "beside".}
#'
#' \item{\code{littleTicks=FALSE}:}{ Logical scalar. Add more fine-grained tick
#' marks.}
#'
#' \item{\code{lwd=2}:}{ Numeric scalar. The line width for the axis
#' elementes.}
#'
#' \item{\code{scale=NULL}:}{ Numeric scalar. If not \code{NULL} a small scale
#' is drawn instead of the full axis, if the value is between 0 and 1 it is
#' interpreted as a fraction of the current plotting region, otherwise as an
#' absolute length value in genomic coordinates.}
#'
#' \item{\code{showId=FALSE}:}{ Logical scalar. Show the optional range
#' highlighting annotation.}
#'
#' \item{\code{showTitle=FALSE}:}{ Logical scalar. Plot a title panel. Defaults
#' to omit the title panel.}
#'
#' \item{\code{ticksAt=NULL}:}{ Numeric scalar. The exact x-position for
#' tickmarks (in base-pairs).}
#'
#' \item{\code{size=NULL}:}{ Numeric scalar. The relative size of the track.
#' Can be overridden in the \code{\link{plotTracks}} function. Defaults to the
#' ideal size based on the other track settings.}
#'
#' \item{\code{col="darkgray"}:}{ Character scalar. The color for the axis
#' lines and tickmarks.}
#'
#' }
#'
#' \bold{\emph{Inherited from class GdObject:}}
#'
#' \describe{
#'
#' \item{\code{alpha=1}:}{ Numeric scalar. The transparency for all track
#' items.}
#'
#' \item{\code{alpha.title=NULL}:}{ Numeric scalar. The transparency for the
#' title panel.}
#'
#' \item{\code{background.panel="transparent"}:}{ Integer or character scalar.
#' The background color of the content panel.}
#'
#' \item{\code{background.legend="transparent"}:}{ Integer or character scalar.
#' The background color for the legend.}
#'
#' \item{\code{cex.axis=NULL}:}{ Numeric scalar. The expansion factor for the
#' axis annotation. Defaults to \code{NULL}, in which case it is automatically
#' determined 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{\linkS4class{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 border
#' color for the title panels}
#'
#' \item{\code{collapse=TRUE}:}{ Boolean controlling whether to collapse the
#' content of the track to accomodate the minimum current device resolution.
#' See \code{\link{collapsing}} for details.}
#'
#' \item{\code{fill="lightgray"}:}{ Integer or character scalar.  Default fill
#' color setting for all plotting elements, unless there is a more specific
#' control defined elsewhere.}
#'
#' \item{\code{fontface.title=2}:}{ Integer or character scalar.  The font face
#' for the title panels.}
#'
#' \item{\code{fontface=1}:}{ Integer or character scalar. The font face for
#' all text, unless a more specific definition exists.}
#'
#' \item{\code{fontfamily.title="sans"}:}{ Integer or character scalar. The
#' font family for the title panels.}
#'
#' \item{\code{fontfamily="sans"}:}{ Integer or character scalar.  The font
#' family for all text, unless a more specific definition exists.}
#'
#' \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{lineheight=1}:}{ Numeric scalar. The font line height for all
#' text, unless a more specific definition exists.}
#'
#' \item{\code{lty.grid="solid"}:}{ Integer or character scalar.  Default line
#' type for grid lines, both when \code{type=="g"} in \code{\linkS4class{DataTrack}}s
#' and when display parameter \code{grid==TRUE}.}
#'
#' \item{\code{lty="solid"}:}{ Numeric scalar. Default line type setting for
#' all plotting elements, unless there is a more specific control defined
#' elsewhere.}
#'
#' \item{\code{lwd.title=1}:}{ Integer scalar. The border width for the title
#' panels}
#'
#' \item{\code{lwd.grid=1}:}{ Numeric scalar. Default line width for grid
#' lines, both when \code{type=="g"} in \code{\linkS4class{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{reverseStrand=FALSE}:}{ Logical scalar. Set up the plotting
#' coordinates in 3' -> 5' direction if \code{TRUE}.  This will effectively
#' mirror the plot on the vertical axis.}
#'
#' \item{\code{rotation.title=90}:}{ 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.}
#'
#' \item{\code{rotation=0}:}{ The rotation angle for all text unless a more
#' specific definiton exists.}
#'
#' \item{\code{showAxis=TRUE}:}{ Boolean controlling whether to plot a y axis
#' (only applies to track types where axes are implemented).}
#'
#' \item{\code{v=-1}:}{ Integer scalar. Parameter controlling the number of
#' vertical grid lines, see \code{\link{panel.grid}} for details.}
#'
#' }
#'
#' }
#'
#' \item{DataTrack:}{
#'
#' \describe{
#'
#' \item{\code{aggregateGroups=FALSE}:}{ Logical scalar. Aggregate the values
#' within a sample group using the aggregation funnction specified in the
#' \code{aggregation} parameter.}
#'
#' \item{\code{aggregation="mean"}:}{ Function or character scalar.  Used to
#' aggregate values in windows or for collapsing overlapping items. The
#' function has to accept a numeric vector as a single input parameter and has
#' to return a numeric scalar with the aggregated value. Alternatively, one of
#' the predefined options \code{mean}, \code{median} \code{sum}, \code{min},
#' \code{max} or \code{extreme} can be supplied as a character scalar. Defaults
#' to \code{mean}.}
#'
#' \item{\code{missingAsZero=TRUE}:}{ Logical scalar. Defines how the missing
#' values are treated in the aggregation procedure with running window. Setting
#' it to \code{TRUE} fills empty positions with zeros, which is default.
#' \code{FALSE} fills empty positions with \code{NA}.}
#'
#' \item{\code{alpha.confint=0.3}:}{ Numeric scalar. The transparency for the
#' confidence intervalls in confint-type plots.}
#'
#' \item{\code{amount=NULL}:}{ Numeric scalar. Amount of jittering in xy-type
#' plots. See \code{\link{panel.xyplot}} for details.}
#'
#' \item{\code{baseline=NULL}:}{ Numeric scalar. Y-axis position of an optional
#' baseline. This parameter has a special meaning for mountain-type and
#' polygon-type plots, see the 'Details' section in
#' \code{\linkS4class{DataTrack}} for more information.}
#'
#' \item{\code{box.legend=FALSE}:}{ Logical scalar. Draw a box around a
#' legend.}
#'
#' \item{\code{box.ratio=1}:}{ Numeric scalar. Parameter controlling the
#' boxplot appearance. See \code{\link{panel.bwplot}} for details.}
#'
#' \item{\code{box.width=NULL}:}{ Numeric scalar. Parameter controlling the
#' boxplot appearance. See \code{\link{panel.bwplot}} for details.}
#'
#' \item{\code{grid=FALSE}:}{ Logical vector. Draw a line grid under the track
#' content.}
#'
#' \item{\code{cex.legend=0.8}:}{ Numeric scalar. The size factor for the
#' legend text.}
#'
#' \item{\code{cex.sampleNames=NULL}:}{ Numeric scalar. The size factor for the
#' sample names text in heatmap or horizon plots.  Defaults to an automatic
#' setting.}
#'
#' \item{\code{cex=0.7}:}{ Numeric scalar. The default pixel size for plotting
#' symbols.}
#'
#' \item{\code{coef=1.5}:}{ Numeric scalar. Parameter controlling the boxplot
#' appearance. See \code{\link{panel.bwplot}} for details.}
#'
#' \item{\code{col.baseline=NULL}:}{ Character scalar. Color for the optional
#' baseline, defaults to the setting of \code{col}.}
#'
#' \item{\code{col.confint=NA}:}{ Character vector. Border colors for the
#' confidence intervals for confint-type plots.}
#'
#' \item{\code{col.boxplotFrame="#808080"}:}{ Character scalar.  Line color of
#' the frame around grouped boxplots.}
#'
#' \item{\code{col.histogram="#808080"}:}{ Character scalar. Line color in
#' histogram-type plots.}
#'
#' \item{\code{col.horizon=NA}:}{ The line color for the segments in the
#' \code{horizon}-type plot. See \code{\link{horizonplot}} for details.}
#'
#' \item{\code{col.mountain=NULL}:}{ Character scalar. Line color in
#' mountain-type and polygon-type plots, defaults to the setting of
#' \code{col}.}
#'
#' \item{\code{col.sampleNames="white"}:}{ Character or integer scalar. The
#' color used for the sample names in heatmap plots.}
#'
#' \item{\code{col=c("#0080ff", "#ff00ff", "darkgreen", "#ff0000", "orange",
#' "#00ff00", "brown")}:}{ Character or integer vector.  The color used for all
#' line and symbol elements, unless there is a more specific control defined
#' elsewhere. Unless \code{groups} are specified, only the first color in the
#' vector is usually regarded.}
#'
#' \item{\code{collapse=FALSE}:}{ Logical scalar. Collapse overlapping ranges
#' and aggregate the underlying data.}
#'
#' \item{\code{degree=1}:}{ Numeric scalar. Parameter controlling the loess
#' calculation for smooth and mountain-type plots.  See
#' \code{\link{panel.loess}} for details.}
#'
#' \item{\code{do.out=TRUE}:}{ Logical scalar. Parameter controlling the
#' boxplot appearance. See \code{\link{panel.bwplot}} for details.}
#'
#' \item{\code{evaluation=50}:}{ Numeric scalar. Parameter controlling the
#' loess calculation for smooth and mountain-type plots. See
#' \code{\link{panel.loess}} for details.}
#'
#' \item{\code{factor=0.5}:}{ Numeric scalar. Factor to control amount of
#' jittering in xy-type plots. See \code{\link{panel.xyplot}} for details.}
#'
#' \item{\code{family="symmetric"}:}{ Character scalar. Parameter controlling
#' the loess calculation for smooth and mountain-type plots. See
#' \code{\link{panel.loess}} for details.}
#'
#' \item{\code{fill.confint=NULL}:}{ Character vector. Fill colors for the
#' confidence intervals for confint-type plots.}
#'
#' \item{\code{fill.histogram=NULL}:}{ Character scalar. Fill color in
#' histogram-type plots, defaults to the setting of \code{fill}.}
#'
#' \item{\code{fill.horizon=c("#B41414", "#E03231", "#F7A99C", "#9FC8DC",
#' "#468CC8", "#0165B3")}:}{ The fill colors for the segments in the
#' \code{horizon}-type plot. This should be a vector of length six, where the
#' first three entries are the colors for positive changes, and the latter
#' three entries are the colors for negative changes. Defaults to a red-blue
#' color scheme. See \code{\link{horizonplot}} for details.}
#'
#' \item{\code{fill.mountain=c("#CCFFFF", "#FFCCFF")}:}{ Character vector of
#' length 2. Fill color in mountain-type and polygon-type plots.}
#'
#' \item{\code{fontface.legend=NULL}:}{ Integer or character scalar. The font
#' face for the legend text.}
#'
#' \item{\code{fontfamily.legend=NULL}:}{ Integer or character scalar. The font
#' family for the legend text.}
#'
#' \item{\code{fontsize.legend=NULL}:}{ Numeric scalar. The pixel size for the
#' legend text.}
#'
#' \item{\code{fontcolor.legend="#808080"}:}{ Integer or character scalar. The
#' font color for the legend text.}
#'
#' \item{\code{gradient=c("#F7FBFF", "#DEEBF7", "#C6DBEF", "#9ECAE1",
#' "#6BAED6", "#4292C6", "#2171B5", "#08519C", "#08306B")}:}{ Character vector.
#' The base colors for the \code{gradient} plotting type or the \code{heatmap}
#' type with a single group. When plotting heatmaps with more than one group,
#' the \code{col} parameter can be used to control the group color scheme,
#' however the gradient will always be from white to 'col' and thus does not
#' offer as much flexibility as this \code{gradient} parameter.}
#'
#' \item{\code{groups=NULL}:}{ Vector coercable to a factor.  Optional sample
#' grouping. See 'Details' section in \code{\linkS4class{DataTrack}} for
#' further information.}
#'
#' \item{\code{horizon.origin=0}:}{ The baseline relative to which changes are
#' indicated on the \code{horizon}-type plot. See \code{\link{horizonplot}} for
#' details.}
#'
#' \item{\code{horizon.scale=NULL}:}{ The scale for each of the segments in the
#' \code{horizon}-type plot. Defaults to 1/3 of the absolute data range. See
#' \code{\link{horizonplot}} for details.}
#'
#' \item{\code{jitter.x=FALSE}:}{ Logical scalar. Toggle on jittering on the x
#' axis in xy-type plots. See \code{\link{panel.xyplot}} for details.}
#'
#' \item{\code{jitter.y=FALSE}:}{ Logical scalar. Toggle off jittering on the y
#' axis in xy-type plots. See \code{\link{panel.xyplot}} for details.}
#'
#' \item{\code{levels.fos=NULL}:}{ Numeric scalar. Parameter controlling the
#' boxplot appearance. See \code{\link{panel.bwplot}} for details.}
#'
#' \item{\code{legend=TRUE}:}{ Boolean triggering the addition of a legend to
#' the track to indicate groups. This only has an effect if at least two groups
#' are present.}
#'
#' \item{\code{lineheight.legend=NULL}:}{ Numeric scalar. The line height for
#' the legend text.}
#'
#' \item{\code{lty.baseline=NULL}:}{ Character or numeric scalar.  Line type of
#' the optional baseline, defaults to the setting of \code{lty}.}
#'
#' \item{\code{lty.mountain=NULL}:}{ Character or numeric scalar.  Line type in
#' mountain-type and polygon-type plots, defaults to the setting of
#' \code{lty}.}
#'
#' \item{\code{lwd.baseline=NULL}:}{ Numeric scalar. Line width of the optional
#' baseline, defaults to the setting of \code{lwd}.}
#'
#' \item{\code{lwd.mountain=NULL}:}{ Numeric scalar. Line width in
#' mountain-type and polygon-type plots, defaults to the setting of
#' \code{lwd}.}
#'
#' \item{\code{min.distance=0}:}{ Numeric scalar. The mimimum distance in pixel
#' below which to collapse ranges.}
#'
#' \item{\code{na.rm=FALSE}:}{ Boolean controlling whether to discard all NA
#' values when plotting or to keep empty spaces for NAs}
#'
#' \item{\code{ncolor=100}:}{ Integer scalar. The number of colors for the
#' 'gradient' plotting type}
#'
#' \item{\code{notch.frac=0.5}:}{ Numeric scalar. Parameter controlling the
#' boxplot appearance. See \code{\link{panel.bwplot}} for details.}
#'
#' \item{\code{notch=FALSE}:}{ Logical scalar. Parameter controlling the
#' boxplot appearance. See \code{\link{panel.bwplot}} for details.}
#'
#' \item{\code{pch=20}:}{ Integer scalar. The type of glyph used for plotting
#' symbols.}
#'
#' \item{\code{separator=0}:}{ Numeric scalar. Number of pixels used to
#' separate individual samples in heatmap- and horizon-type plots.}
#'
#' \item{\code{showColorBar=TRUE}:}{ Boolean. Indicate the data range color
#' mapping in the axis for 'heatmap' or 'gradient' types.}
#'
#' \item{\code{showSampleNames=FALSE}:}{ Boolean. Display the names of the
#' individual samples in a heatmap or a horizon plot.}
#'
#' \item{\code{size=NULL}:}{ Numeric scalar. The relative size of the track.
#' Can be overridden in the \code{\link{plotTracks}} function. By default the
#' size will be set automatically based on the selected plotting type.}
#'
#' \item{\code{span=0.2}:}{ Numeric scalar. Parameter controlling the loess
#' calculation for smooth and mountain-type plots.  See
#' \code{\link{panel.loess}} for details.}
#'
#' \item{\code{stackedBars=TRUE}:}{ Logical scalar. When there are several data
#' groups, draw the histogram-type plots as stacked barplots or grouped side by
#' side.}
#'
#' \item{\code{stats=X[[i]]}:}{ Function. Parameter controlling the boxplot
#' appearance. See \code{\link{panel.bwplot}} for details.}
#'
#' \item{\code{transformation=NULL}:}{ Function. Applied to the data matrix
#' prior to plotting or when calling the \code{score} method. The function
#' should accept exactly one input argument and its return value needs to be a
#' numeric vector which can be coerced back into a data matrix of identical
#' dimensionality as the input data.}
#'
#' \item{\code{type="p"}:}{ Character vector. The plot type, one or several in
#' \code{p},\code{l}, \code{b}, \code{a}, \code{a_confint}, \code{s}, \code{g},
#' \code{r}, \code{S}, \code{confint}, \code{smooth}, \code{histogram},
#' \code{mountain}, \code{polygon}, \code{h}, \code{boxplot}, \code{gradient},
#' \code{heatmap}, \code{horizon}. See 'Details' section in
#' \code{\linkS4class{DataTrack}} for more information on the individual
#' plotting types.}
#'
#' \item{\code{varwidth=FALSE}:}{ Logical scalar. Parameter controlling the
#' boxplot appearance. See \code{\link{panel.bwplot}} for details.}
#'
#' \item{\code{window=NULL}:}{ Numeric or character scalar.  Aggregate the rows
#' values of the data matrix to \code{window} equally sized slices on the data
#' range using the method defined in \code{aggregation}. If negative, apply a
#' running window of size \code{windowSize} using the same aggregation method.
#' Alternatively, the special value \code{auto} causes the function to
#' determine the optimal window size to avoid overplotting, and \code{fixed}
#' uses fixed-size windows of size \code{windowSize}.}
#'
#' \item{\code{windowSize=NULL}:}{ Numeric scalar. The size of the running
#' window when the value of \code{window} is negative.}
#'
#' \item{\code{ylim=NULL}:}{ Numeric vector of length 2. The range of the
#' y-axis scale.}
#'
#' \item{\code{yTicksAt=NULL}:}{ Numeric vector. The points at which y-axis
#' tick-marks are to be drawn. By default, when \code{NULL}, tickmark locations
#' are computed.}
#'
#' }
#'
#' \bold{\emph{Inherited from class GdObject:}}
#'
#' \describe{
#'
#' \item{\code{alpha=1}:}{ Numeric scalar. The transparency for all track
#' items.}
#'
#' \item{\code{alpha.title=NULL}:}{ Numeric scalar. The transparency for the
#' title panel.}
#'
#' \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 panel.}
#'
#' \item{\code{background.legend="transparent"}:}{ Integer or character scalar.
#' The background color for the legend.}
#'
#' \item{\code{cex.axis=NULL}:}{ Numeric scalar. The expansion factor for the
#' axis annotation. Defaults to \code{NULL}, in which case it is automatically
#' determined 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.border.title="white"}:}{ Integer or character scalar. The
#' border color for the title panels.}
#'
#' \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{\linkS4class{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 border
#' color for the title panels}
#'
#' \item{\code{fill="lightgray"}:}{ Integer or character scalar.  Default fill
#' color setting for all plotting elements, unless there is a more specific
#' control defined elsewhere.}
#'
#' \item{\code{fontcolor="black"}:}{ Integer or character scalar.  The font
#' color for all text, unless a more specific definition exists.}
#'
#' \item{\code{fontface.title=2}:}{ Integer or character scalar.  The font face
#' for the title panels.}
#'
#' \item{\code{fontface=1}:}{ Integer or character scalar. The font face for
#' all text, unless a more specific definition exists.}
#'
#' \item{\code{fontfamily.title="sans"}:}{ Integer or character scalar. The
#' font family for the title panels.}
#'
#' \item{\code{fontfamily="sans"}:}{ Integer or character scalar.  The font
#' family for all text, unless a more specific definition exists.}
#'
#' \item{\code{fontsize=12}:}{ Numeric scalar. The font size for all text,
#' unless a more specific definition exists.}
#'
#' \item{\code{frame=FALSE}:}{ Boolean. Draw a frame around the track when
#' plotting.}
#'
#' \item{\code{h=-1}:}{ Integer scalar. Parameter controlling the number of
#' horizontal grid lines, see \code{\link{panel.grid}} for details.}
#'
#' \item{\code{lineheight=1}:}{ Numeric scalar. The font line height for all
#' text, unless a more specific definition exists.}
#'
#' \item{\code{lty.grid="solid"}:}{ Integer or character scalar.  Default line
#' type for grid lines, both when \code{type=="g"} in \code{\linkS4class{DataTrack}}s
#' and when display parameter \code{grid==TRUE}.}
#'
#' \item{\code{lty="solid"}:}{ Numeric scalar. Default line type setting for
#' all plotting elements, unless there is a more specific control defined
#' elsewhere.}
#'
#' \item{\code{lwd.border.title=1}:}{ Integer scalar. The border width for the
#' title panels.}
#'
#' \item{\code{lwd.title=1}:}{ Integer scalar. The border width for the title
#' panels}
#'
#' \item{\code{lwd.grid=1}:}{ Numeric scalar. Default line width for grid
#' lines, both when \code{type=="g"} in \code{\linkS4class{DataTrack}}s and when
#' display parameter \code{grid==TRUE}.}
#'
#' \item{\code{lwd=1}:}{ Numeric scalar. Default line width setting for all
#' plotting elements, unless there is a more specific control defined
#' elsewhere.}
#'
#' \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{reverseStrand=FALSE}:}{ Logical scalar. Set up the plotting
#' coordinates in 3' -> 5' direction if \code{TRUE}.  This will effectively
#' mirror the plot on the vertical axis.}
#'
#' \item{\code{rotation.title=90}:}{ 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.}
#'
#' \item{\code{rotation=0}:}{ The rotation angle for all text unless a more
#' specific definiton exists.}
#'
#' \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.}
#'
#' }
#'
#' }
#'
#' \item{IdeogramTrack:}{
#'
#' \describe{
#'
#' \item{\code{background.title="transparent"}:}{ Character scalar.  The
#' background color for the title panel. Defaults to omit the background.}
#'
#' \item{\code{bevel=0.45}:}{ Numeric scalar, between 0 and 1.  The level of
#' smoothness for the two ends of the ideogram.}
#'
#' \item{\code{centromereShape="triangle"}:}{ Character scalar.  The shape of
#' the centromere. Only "triangle" or "circle" is accepted. Default to
#' "triangle"}
#'
#' \item{\code{cex.bands=0.7}:}{ Numeric scalar. The font expansion factor for
#' the chromosome band identifier text.}
#'
#' \item{\code{cex=0.8}:}{ Numeric scalar. The overall font expansion factor
#' for the chromosome name text.}
#'
#' \item{\code{col="red"}:}{ Character scalar. The border color used for the
#' highlighting of the currently displayed genomic region.}
#'
#' \item{\code{col.border.title="transparent"}:}{ Integer or character scalar.
#' The border color for the title panels.}
#'
#' \item{\code{lwd.border.title=1}:}{ Integer scalar. The border width for the
#' title panels.}
#'
#' \item{\code{fill="#FFE3E6"}:}{ Character scalar. The fill color used for the
#' highlighting of the currently displayed genomic region.}
#'
#' \item{\code{fontface=1}:}{ Character scalar. The font face for the
#' chromosome name text.}
#'
#' \item{\code{fontfamily="sans"}:}{ Character scalar. The font family for the
#' chromosome name text.}
#'
#' \item{\code{fontcolor="#808080"}:}{ Character scalar. The font color for the
#' chromosome name text.}
#'
#' \item{\code{fontsize=10}:}{ Numeric scalar. The font size for the chromosome
#' name text.}
#'
#' \item{\code{outline=FALSE}:}{ Logical scalar. Add borders to the individual
#' chromosome staining bands.}
#'
#' \item{\code{showBandId=FALSE}:}{ Logical scalar. Show the identifier for the
#' chromosome bands if there is space for it.}
#'
#' \item{\code{lty=1}:}{ Character or integer scalar. The line type used for
#' the highlighting of the currently displayed genomic region.}
#'
#' \item{\code{lwd=1}:}{ Numeric scalar. The line width used for the
#' highlighting of the currently displayed genomic region.}
#'
#' \item{\code{showId=TRUE}:}{ Logical scalar. Indicate the chromosome name
#' next to the ideogram.}
#'
#' \item{\code{showTitle=FALSE}:}{ Logical scalar. Plot a title panel. Defaults
#' to omit the title panel.}
#'
#' \item{\code{size=NULL}:}{ Numeric scalar. The relative size of the track.
#' Defaults to automatic size setting. Can also be overridden in the
#' \code{\link{plotTracks}} function.}
#'
#' }
#'
#' \bold{\emph{Inherited from class GdObject:}}
#'
#' \describe{
#'
#' \item{\code{alpha=1}:}{ Numeric scalar. The transparency for all track
#' items.}
#'
#' \item{\code{alpha.title=NULL}:}{ Numeric scalar. The transparency for the
#' title panel.}
#'
#' \item{\code{background.panel="transparent"}:}{ Integer or character scalar.
#' The background color of the content panel.}
#'
#' \item{\code{background.legend="transparent"}:}{ Integer or character scalar.
#' The background color for the legend.}
#'
#' \item{\code{cex.axis=NULL}:}{ Numeric scalar. The expansion factor for the
#' axis annotation. Defaults to \code{NULL}, in which case it is automatically
#' determined 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{\linkS4class{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 border
#' color for the title panels}
#'
#' \item{\code{collapse=TRUE}:}{ Boolean controlling whether 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{lineheight=1}:}{ Numeric scalar. The font line height for all
#' text, unless a more specific definition exists.}
#'
#' \item{\code{lty.grid="solid"}:}{ Integer or character scalar.  Default line
#' type for grid lines, both when \code{type=="g"} in \code{\linkS4class{DataTrack}}s
#' and when display parameter \code{grid==TRUE}.}
#'
#' \item{\code{lwd.title=1}:}{ Integer scalar. The border width for the title
#' panels}
#'
#' \item{\code{lwd.grid=1}:}{ Numeric scalar. Default line width for grid
#' lines, both when \code{type=="g"} in \code{\linkS4class{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{reverseStrand=FALSE}:}{ Logical scalar. Set up the plotting
#' coordinates in 3' -> 5' direction if \code{TRUE}.  This will effectively
#' mirror the plot on the vertical axis.}
#'
#' \item{\code{rotation.title=90}:}{ 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.}
#'
#' \item{\code{rotation=0}:}{ The rotation angle for all text unless a more
#' specific definiton exists.}
#'
#' \item{\code{showAxis=TRUE}:}{ Boolean controlling whether to plot a y axis
#' (only applies to track types where axes are implemented).}
#'
#' \item{\code{v=-1}:}{ Integer scalar. Parameter controlling the number of
#' vertical grid lines, see \code{\link{panel.grid}} for details.}
#'
#' }
#'
#' }
#'
#' \item{AnnotationTrack:}{
#'
#' \describe{
#'
#' \item{\code{arrowHeadWidth=30}:}{ Numeric scalar. The width of the arrow
#' head in pixels if \code{shape} is \code{fixedArrow}.}
#'
#' \item{\code{arrowHeadMaxWidth=40}:}{ Numeric scalar. The maximum width of
#' the arrow head in pixels if \code{shape} is \code{arrow}.}
#'
#' \item{\code{cex.group=0.6}:}{ Numeric scalar. The font expansion factor for
#' the group-level annotation.}
#'
#' \item{\code{cex=1}:}{ Numeric scalar. The font expansion factor for item
#' identifiers.}
#'
#' \item{\code{col.line="darkgray"}:}{ Character scalar. The color used for
#' connecting lines between grouped items. Defaults to a light gray, but if set
#' to \code{NULL} the same color as for the first item in the group is used.}
#'
#' \item{\code{col="transparent"}:}{ Character or integer scalar.  The border
#' color for all track items.}
#'
#' \item{\code{featureAnnotation=NULL}:}{ Character scalar. Add annotation
#' information to the individual track elements. This can be a value in
#' \code{id}, \code{group} or \code{feature}.  Defaults to \code{id}. Only
#' works if \code{showFeatureId} is not \code{FALSE}.}
#'
#' \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{fontfamily.group="sans"}:}{ Character scalar. The font family
#' for the group-level annotation.}
#'
#' \item{\code{fontcolor.group="#808080"}:}{ Character or integer scalar. The
#' font color for the group-level annotation.}
#'
#' \item{\code{fontcolor.item="white"}:}{ Character or integer scalar. The font
#' color for item identifiers.}
#'
#' \item{\code{fontface.group=2}:}{ Numeric scalar. The font face for the
#' group-level annotation.}
#'
#' \item{\code{fontsize.group=12}:}{ Numeric scalar. The font size for the
#' group-level annotation.}
#'
#' \item{\code{groupAnnotation=NULL}:}{ Character scalar. Add annotation
#' information as group labels. This can be a value in \code{id}, \code{group}
#' or \code{feature}. Defaults to \code{group}. Only works if \code{showId} is
#' not \code{FALSE}.}
#'
#' \item{\code{just.group="left"}:}{ Character scalar. the justification of
#' group labels. Either \code{left}, \code{right}, \code{above} or
#' \code{below}.}
#'
#' \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{mergeGroups=FALSE}:}{ Logical scalar. Merge fully overlapping
#' groups if \code{collapse==TRUE}.}
#'
#' \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. For feathered
#' bars indicating the strandedness of grouped items this also controls the
#' height of the arrow feathers.}
#'
#' \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{rotation=0}:}{ Numeric scalar. The degree of text rotation for
#' item identifiers.}
#'
#' \item{\code{rotation.group=0}:}{ Numeric scalar. The degree of text rotation
#' for group labels.}
#'
#' \item{\code{rotation.item=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{fixedArrow}, \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.}
#'
#' }
#'
#' \bold{\emph{Inherited from class StackedTrack:}}
#'
#' \describe{
#'
#' \item{\code{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.}
#'
#' \item{\code{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.}
#'
#' }
#'
#' \bold{\emph{Inherited from class GdObject:}}
#'
#' \describe{
#'
#' \item{\code{alpha=1}:}{ Numeric scalar. The transparency for all track
#' items.}
#'
#' \item{\code{alpha.title=NULL}:}{ Numeric scalar. The transparency for the
#' title panel.}
#'
#' \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 panel.}
#'
#' \item{\code{background.legend="transparent"}:}{ Integer or character scalar.
#' The background color for the legend.}
#'
#' \item{\code{cex.axis=NULL}:}{ Numeric scalar. The expansion factor for the
#' axis annotation. Defaults to \code{NULL}, in which case it is automatically
#' determined 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.border.title="white"}:}{ Integer or character scalar. The
#' border color for the title panels.}
#'
#' \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{\linkS4class{DataTrack}}s and when display parameter \code{grid==TRUE}.}
#'
#' \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 border
#' color for the title panels}
#'
#' \item{\code{collapse=TRUE}:}{ Boolean controlling whether to collapse the
#' content of the track to accomodate the minimum current device resolution.
#' See \code{\link{collapsing}} for details.}
#'
#' \item{\code{fontcolor="black"}:}{ Integer or character scalar.  The font
#' color for all text, unless a more specific definition exists.}
#'
#' \item{\code{fontface.title=2}:}{ Integer or character scalar.  The font face
#' for the title panels.}
#'
#' \item{\code{fontface=1}:}{ Integer or character scalar. The font face for
#' all text, unless a more specific definition exists.}
#'
#' \item{\code{fontfamily.title="sans"}:}{ Integer or character scalar. The
#' font family for the title panels.}
#'
#' \item{\code{fontfamily="sans"}:}{ Integer or character scalar.  The font
#' family for all text, unless a more specific definition exists.}
#'
#' \item{\code{fontsize=12}:}{ Numeric scalar. The font size for all text,
#' unless a more specific definition exists.}
#'
#' \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{\linkS4class{DataTrack}}s
#' and when display parameter \code{grid==TRUE}.}
#'
#' \item{\code{lwd.border.title=1}:}{ Integer scalar. The border width for the
#' title panels.}
#'
#' \item{\code{lwd.title=1}:}{ Integer scalar. The border width for the title
#' panels}
#'
#' \item{\code{lwd.grid=1}:}{ Numeric scalar. Default line width for grid
#' lines, both when \code{type=="g"} in \code{\linkS4class{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{reverseStrand=FALSE}:}{ Logical scalar. Set up the plotting
#' coordinates in 3' -> 5' direction if \code{TRUE}.  This will effectively
#' mirror the plot on the vertical axis.}
#'
#' \item{\code{rotation.title=90}:}{ 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.}
#'
#' \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.}
#'
#' }
#'
#' }
#'
#' \item{GeneRegionTrack:}{
#'
#' \describe{
#'
#' \item{\code{arrowHeadWidth=10}:}{ Numeric scalar. The width of the arrow
#' head in pixels if \code{shape} is \code{fixedArrow}.}
#'
#' \item{\code{arrowHeadMaxWidth=20}:}{ Numeric scalar. The maximum width of
#' the arrow head in pixels if \code{shape} is \code{arrow}.}
#'
#' \item{\code{col=NULL}:}{ Character or integer scalar. The border color for
#' all track items. Defaults to using the same color as in \code{fill}, also
#' taking into account different track \code{features}.}
#'
#' \item{\code{collapseTranscripts=FALSE}:}{ Logical or character scalar. Can
#' be one in \code{gene}, \code{longest}, \code{shortest} or \code{meta}. Merge
#' all transcripts of the same gene into one single gene model. In the case of
#' \code{gene} (or \code{TRUE}), this will only keep the start location of the
#' first exon and the end location of the last exon from all transcripts of the
#' gene. For \code{shortest} and \code{longest}, only the longest or shortest
#' transcript model is retained.  For \code{meta}, a meta-transcript containing
#' the union of all exons is formed (essentially identical to the operation
#' \code{reduce(geneModel)}).}
#'
#' \item{\code{exonAnnotation=NULL}:}{ Character scalar. Add annotation
#' information to the individual exon models. This can be a value in
#' \code{symbol}, \code{gene}, \code{transcript}, \code{exon} or
#' \code{feature}. Defaults to \code{exon}. Only works if \code{showExonId} is
#' not \code{FALSE}.}
#'
#' \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{min.distance=0}:}{ Numeric scalar. The minimum pixel distance
#' before collapsing range items, only if \code{collapse==TRUE}. See
#' \code{\link{collapsing}} for details. Note that a value larger than 0 may
#' lead to UTR regions being merged to CDS regions, which in most cases is not
#' particularly useful.}
#'
#' \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=NULL}:}{ Logical scalar. Control whether to plot the
#' individual exon identifiers.}
#'
#' \item{\code{thinBoxFeature=c("utr", "ncRNA", "utr3", "utr5", "3UTR",
#' "5UTR", "miRNA", "lincRNA", "three_prime_UTR", "five_prime_UTR")}:}{ Character
#' vector. A listing of feature types that should be drawn with thin boxes.
#' Typically those are non-coding elements.}
#'
#' \item{\code{transcriptAnnotation=NULL}:}{ Character scalar.  Add annotation
#' information as transcript labels. This can be a value in \code{symbol},
#' \code{gene}, \code{transcript}, \code{exon} or \code{feature}. Defaults to
#' \code{symbol}.  Only works if \code{showId} is not \code{FALSE}.}
#'
#' }
#'
#' \bold{\emph{Inherited from class AnnotationTrack:}}
#'
#' \describe{
#'
#' \item{\code{cex.group=0.6}:}{ Numeric scalar. The font expansion factor for
#' the group-level annotation.}
#'
#' \item{\code{cex=1}:}{ Numeric scalar. The font expansion factor for item
#' identifiers.}
#'
#' \item{\code{col.line="darkgray"}:}{ Character scalar. The color used for
#' connecting lines between grouped items. Defaults to a light gray, but if set
#' to \code{NULL} the same color as for the first item in the group is used.}
#'
#' \item{\code{featureAnnotation=NULL}:}{ Character scalar. Add annotation
#' information to the individual track elements. This can be a value in
#' \code{id}, \code{group} or \code{feature}.  Defaults to \code{id}. Only
#' works if \code{showFeatureId} is not \code{FALSE}.}
#'
#' \item{\code{fontfamily.group="sans"}:}{ Character scalar. The font family
#' for the group-level annotation.}
#'
#' \item{\code{fontcolor.group="#808080"}:}{ Character or integer scalar. The
#' font color for the group-level annotation.}
#'
#' \item{\code{fontcolor.item="white"}:}{ Character or integer scalar. The font
#' color for item identifiers.}
#'
#' \item{\code{fontface.group=2}:}{ Numeric scalar. The font face for the
#' group-level annotation.}
#'
#' \item{\code{fontsize.group=12}:}{ Numeric scalar. The font size for the
#' group-level annotation.}
#'
#' \item{\code{groupAnnotation=NULL}:}{ Character scalar. Add annotation
#' information as group labels. This can be a value in \code{id}, \code{group}
#' or \code{feature}. Defaults to \code{group}. Only works if \code{showId} is
#' not \code{FALSE}.}
#'
#' \item{\code{just.group="left"}:}{ Character scalar. the justification of
#' group labels. Either \code{left}, \code{right}, \code{above} or
#' \code{below}.}
#'
#' \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{mergeGroups=FALSE}:}{ Logical scalar. Merge fully overlapping
#' groups if \code{collapse==TRUE}.}
#'
#' \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. For feathered
#' bars indicating the strandedness of grouped items this also controls the
#' height of the arrow feathers.}
#'
#' \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{rotation=0}:}{ Numeric scalar. The degree of text rotation for
#' item identifiers.}
#'
#' \item{\code{rotation.group=0}:}{ Numeric scalar. The degree of text rotation
#' for group labels.}
#'
#' \item{\code{rotation.item=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.}
#'
#' }
#'
#' \bold{\emph{Inherited from class StackedTrack:}}
#'
#' \describe{
#'
#' \item{\code{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.}
#'
#' \item{\code{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.}
#'
#' }
#'
#' \bold{\emph{Inherited from class GdObject:}}
#'
#' \describe{
#'
#' \item{\code{alpha=1}:}{ Numeric scalar. The transparency for all track
#' items.}
#'
#' \item{\code{alpha.title=NULL}:}{ Numeric scalar. The transparency for the
#' title panel.}
#'
#' \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 panel.}
#'
#' \item{\code{background.legend="transparent"}:}{ Integer or character scalar.
#' The background color for the legend.}
#'
#' \item{\code{cex.axis=NULL}:}{ Numeric scalar. The expansion factor for the
#' axis annotation. Defaults to \code{NULL}, in which case it is automatically
#' determined 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.border.title="white"}:}{ Integer or character scalar. The
#' border color for the title panels.}
#'
#' \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{\linkS4class{DataTrack}}s and when display parameter \code{grid==TRUE}.}
#'
#' \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 border
#' color for the title panels}
#'
#' \item{\code{collapse=TRUE}:}{ Boolean controlling whether to collapse the
#' content of the track to accomodate the minimum current device resolution.
#' See \code{\link{collapsing}} for details.}
#'
#' \item{\code{fontcolor="black"}:}{ Integer or character scalar.  The font
#' color for all text, unless a more specific definition exists.}
#'
#' \item{\code{fontface.title=2}:}{ Integer or character scalar.  The font face
#' for the title panels.}
#'
#' \item{\code{fontface=1}:}{ Integer or character scalar. The font face for
#' all text, unless a more specific definition exists.}
#'
#' \item{\code{fontfamily.title="sans"}:}{ Integer or character scalar. The
#' font family for the title panels.}
#'
#' \item{\code{fontfamily="sans"}:}{ Integer or character scalar.  The font
#' family for all text, unless a more specific definition exists.}
#'
#' \item{\code{fontsize=12}:}{ Numeric scalar. The font size for all text,
#' unless a more specific definition exists.}
#'
#' \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{\linkS4class{DataTrack}}s
#' and when display parameter \code{grid==TRUE}.}
#'
#' \item{\code{lwd.border.title=1}:}{ Integer scalar. The border width for the
#' title panels.}
#'
#' \item{\code{lwd.title=1}:}{ Integer scalar. The border width for the title
#' panels}
#'
#' \item{\code{lwd.grid=1}:}{ Numeric scalar. Default line width for grid
#' lines, both when \code{type=="g"} in \code{\linkS4class{DataTrack}}s and when
#' display parameter \code{grid==TRUE}.}
#'
#' \item{\code{reverseStrand=FALSE}:}{ Logical scalar. Set up the plotting
#' coordinates in 3' -> 5' direction if \code{TRUE}.  This will effectively
#' mirror the plot on the vertical axis.}
#'
#' \item{\code{rotation.title=90}:}{ 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.}
#'
#' \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.}
#'
#' }
#'
#' }
#'
#' \item{BiomartGeneRegionTrack:}{
#'
#' \describe{
#'
#' \item{\code{C_segment="burlywood4"}:}{ Character or integer scalar. Fill
#' color for annotation objects of type 'C_segment'.}
#'
#' \item{\code{D_segment="lightblue"}:}{ Character or integer scalar. Fill
#' color for annotation objects of type 'C_segment'.}
#'
#' \item{\code{J_segment="dodgerblue2"}:}{ Character or integer scalar. Fill
#' color for annotation objects of type 'C_segment'.}
#'
#' \item{\code{Mt_rRNA="yellow"}:}{ Character or integer scalar.  Fill color
#' for annotation objects of type 'Mt_rRNA'.}
#'
#' \item{\code{Mt_tRNA="darkgoldenrod"}:}{ Character or integer scalar. Fill
#' color for annotation objects of type 'Mt_tRNA'.}
#'
#' \item{\code{Mt_tRNA_pseudogene="darkgoldenrod1"}:}{ Character or integer
#' scalar. Fill color for annotation objects of type 'Mt_tRNA_pseudogene'.}
#'
#' \item{\code{V_segment="aquamarine"}:}{ Character or integer scalar. Fill
#' color for annotation objects of type 'V_segment'.}
#'
#' \item{\code{miRNA="cornflowerblue"}:}{ Character or integer scalar. Fill
#' color for annotation objects of type 'L_segment'.}
#'
#' \item{\code{miRNA_pseudogene="cornsilk"}:}{ Character or integer scalar.
#' Fill color for annotation objects of type 'miRNA_pseudogene'.}
#'
#' \item{\code{misc_RNA="cornsilk3"}:}{ Character or integer scalar. Fill color
#' for annotation objects of type 'misc_RNA'.}
#'
#' \item{\code{misc_RNA_pseudogene="cornsilk4"}:}{ Character or integer scalar.
#' Fill color for annotation objects of type 'misc_RNA_pseudogene'.}
#'
#' \item{\code{protein_coding="#FFD58A"}:}{ Character or integer scalar. Fill
#' color for annotation objects of type 'protein_coding'.}
#'
#' \item{\code{pseudogene="brown1"}:}{ Character or integer scalar.  Fill color
#' for annotation objects of type 'pseudogene'.}
#'
#' \item{\code{rRNA="darkolivegreen1"}:}{ Character or integer scalar. Fill
#' color for annotation objects of type 'rRNA'.}
#'
#' \item{\code{rRNA_pseudogene="darkolivegreen"}:}{ Character or integer
#' scalar. Fill color for annotation objects of type 'rRNA_pseudogene'.}
#'
#' \item{\code{retrotransposed="blueviolet"}:}{ Character or integer scalar.
#' Fill color for annotation objects of type 'retrotransposed'.}
#'
#' \item{\code{scRNA="gold4"}:}{ Character or integer scalar. Fill color for
#' annotation objects of type 'scRNA'.}
#'
#' \item{\code{scRNA_pseudogene="darkorange2"}:}{ Character or integer scalar.
#' Fill color for annotation objects of type 'scRNA_pseudogene'.}
#'
#' \item{\code{snRNA="coral"}:}{ Character or integer scalar. Fill color for
#' annotation objects of type 'snRNA'.}
#'
#' \item{\code{snRNA_pseudogene="coral3"}:}{ Character or integer scalar. Fill
#' color for annotation objects of type 'snRNA_pseudogene'.}
#'
#' \item{\code{snoRNA="cyan"}:}{ Character or integer scalar. Fill color for
#' annotation objects of type 'snoRNA'.}
#'
#' \item{\code{snoRNA_pseudogene="cyan2"}:}{ Character or integer scalar. Fill
#' color for annotation objects of type 'snoRNA_pseudogene'.}
#'
#' \item{\code{tRNA_pseudogene="antiquewhite3"}:}{ Character or integer scalar.
#' Fill color for annotation objects of type 'tRNA_pseudogene'.}
#'
#' \item{\code{utr3="#FFD58A"}:}{ Character or integer scalar.  Fill color for
#' annotation objects of type 'utr3'.}
#'
#' \item{\code{utr5="#FFD58A"}:}{ Character or integer scalar.  Fill color for
#' annotation objects of type 'utr5'.}
#'
#' \item{\code{verbose=FALSE}:}{ Logical scalar. Report data loading events
#' from Bioamart or retrieval from cache.}
#'
#' }
#'
#' \bold{\emph{Inherited from class GeneRegionTrack:}}
#'
#' \describe{
#'
#' \item{\code{arrowHeadWidth=10}:}{ Numeric scalar. The width of the arrow
#' head in pixels if \code{shape} is \code{fixedArrow}.}
#'
#' \item{\code{arrowHeadMaxWidth=20}:}{ Numeric scalar. The maximum width of
#' the arrow head in pixels if \code{shape} is \code{arrow}.}
#'
#' \item{\code{col=NULL}:}{ Character or integer scalar. The border color for
#' all track items. Defaults to using the same color as in \code{fill}, also
#' taking into account different track \code{features}.}
#'
#' \item{\code{collapseTranscripts=FALSE}:}{ Logical or character scalar. Can
#' be one in \code{gene}, \code{longest}, \code{shortest} or \code{meta}. Merge
#' all transcripts of the same gene into one single gene model. In the case of
#' \code{gene} (or \code{TRUE}), this will only keep the start location of the
#' first exon and the end location of the last exon from all transcripts of the
#' gene. For \code{shortest} and \code{longest}, only the longest or shortest
#' transcript model is retained.  For \code{meta}, a meta-transcript containing
#' the union of all exons is formed (essentially identical to the operation
#' \code{reduce(geneModel)}).}
#'
#' \item{\code{exonAnnotation=NULL}:}{ Character scalar. Add annotation
#' information to the individual exon models. This can be a value in
#' \code{symbol}, \code{gene}, \code{transcript}, \code{exon} or
#' \code{feature}. Defaults to \code{exon}. Only works if \code{showExonId} is
#' not \code{FALSE}.}
#'
#' \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{min.distance=0}:}{ Numeric scalar. The minimum pixel distance
#' before collapsing range items, only if \code{collapse==TRUE}. See
#' \code{\link{collapsing}} for details. Note that a value larger than 0 may
#' lead to UTR regions being merged to CDS regions, which in most cases is not
#' particularly useful.}
#'
#' \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=NULL}:}{ Logical scalar. Control whether to plot the
#' individual exon identifiers.}
#'
#' \item{\code{thinBoxFeature=c("utr", "ncRNA", "utr3", "utr5", "3UTR",
#' "5UTR", "miRNA", "lincRNA", "three_prime_UTR", "five_prime_UTR")}:}{ Character
#' vector. A listing of feature types that should be drawn with thin boxes.
#' Typically those are non-coding elements.}
#'
#' \item{\code{transcriptAnnotation=NULL}:}{ Character scalar.  Add annotation
#' information as transcript labels. This can be a value in \code{symbol},
#' \code{gene}, \code{transcript}, \code{exon} or \code{feature}. Defaults to
#' \code{symbol}.  Only works if \code{showId} is not \code{FALSE}.}
#'
#' }
#'
#' \bold{\emph{Inherited from class AnnotationTrack:}}
#'
#' \describe{
#'
#' \item{\code{cex.group=0.6}:}{ Numeric scalar. The font expansion factor for
#' the group-level annotation.}
#'
#' \item{\code{cex=1}:}{ Numeric scalar. The font expansion factor for item
#' identifiers.}
#'
#' \item{\code{col.line="darkgray"}:}{ Character scalar. The color used for
#' connecting lines between grouped items. Defaults to a light gray, but if set
#' to \code{NULL} the same color as for the first item in the group is used.}
#'
#' \item{\code{featureAnnotation=NULL}:}{ Character scalar. Add annotation
#' information to the individual track elements. This can be a value in
#' \code{id}, \code{group} or \code{feature}.  Defaults to \code{id}. Only
#' works if \code{showFeatureId} is not \code{FALSE}.}
#'
#' \item{\code{fontfamily.group="sans"}:}{ Character scalar. The font family
#' for the group-level annotation.}
#'
#' \item{\code{fontcolor.group="#808080"}:}{ Character or integer scalar. The
#' font color for the group-level annotation.}
#'
#' \item{\code{fontcolor.item="white"}:}{ Character or integer scalar. The font
#' color for item identifiers.}
#'
#' \item{\code{fontface.group=2}:}{ Numeric scalar. The font face for the
#' group-level annotation.}
#'
#' \item{\code{fontsize.group=12}:}{ Numeric scalar. The font size for the
#' group-level annotation.}
#'
#' \item{\code{groupAnnotation=NULL}:}{ Character scalar. Add annotation
#' information as group labels. This can be a value in \code{id}, \code{group}
#' or \code{feature}. Defaults to \code{group}. Only works if \code{showId} is
#' not \code{FALSE}.}
#'
#' \item{\code{just.group="left"}:}{ Character scalar. the justification of
#' group labels. Either \code{left}, \code{right}, \code{above} or
#' \code{below}.}
#'
#' \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{mergeGroups=FALSE}:}{ Logical scalar. Merge fully overlapping
#' groups if \code{collapse==TRUE}.}
#'
#' \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. For feathered
#' bars indicating the strandedness of grouped items this also controls the
#' height of the arrow feathers.}
#'
#' \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{rotation=0}:}{ Numeric scalar. The degree of text rotation for
#' item identifiers.}
#'
#' \item{\code{rotation.group=0}:}{ Numeric scalar. The degree of text rotation
#' for group labels.}
#'
#' \item{\code{rotation.item=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.}
#'
#' }
#'
#' \bold{\emph{Inherited from class StackedTrack:}}
#'
#' \describe{
#'
#' \item{\code{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.}
#'
#' \item{\code{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.}
#'
#' }
#'
#' \bold{\emph{Inherited from class GdObject:}}
#'
#' \describe{
#'
#' \item{\code{alpha=1}:}{ Numeric scalar. The transparency for all track
#' items.}
#'
#' \item{\code{alpha.title=NULL}:}{ Numeric scalar. The transparency for the
#' title panel.}
#'
#' \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 panel.}
#'
#' \item{\code{background.legend="transparent"}:}{ Integer or character scalar.
#' The background color for the legend.}
#'
#' \item{\code{cex.axis=NULL}:}{ Numeric scalar. The expansion factor for the
#' axis annotation. Defaults to \code{NULL}, in which case it is automatically
#' determined 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.border.title="white"}:}{ Integer or character scalar. The
#' border color for the title panels.}
#'
#' \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{\linkS4class{DataTrack}}s and when display parameter \code{grid==TRUE}.}
#'
#' \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 border
#' color for the title panels}
#'
#' \item{\code{collapse=TRUE}:}{ Boolean controlling whether to collapse the
#' content of the track to accomodate the minimum current device resolution.
#' See \code{\link{collapsing}} for details.}
#'
#' \item{\code{fontcolor="black"}:}{ Integer or character scalar.  The font
#' color for all text, unless a more specific definition exists.}
#'
#' \item{\code{fontface.title=2}:}{ Integer or character scalar.  The font face
#' for the title panels.}
#'
#' \item{\code{fontface=1}:}{ Integer or character scalar. The font face for
#' all text, unless a more specific definition exists.}
#'
#' \item{\code{fontfamily.title="sans"}:}{ Integer or character scalar. The
#' font family for the title panels.}
#'
#' \item{\code{fontfamily="sans"}:}{ Integer or character scalar.  The font
#' family for all text, unless a more specific definition exists.}
#'
#' \item{\code{fontsize=12}:}{ Numeric scalar. The font size for all text,
#' unless a more specific definition exists.}
#'
#' \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{\linkS4class{DataTrack}}s
#' and when display parameter \code{grid==TRUE}.}
#'
#' \item{\code{lwd.border.title=1}:}{ Integer scalar. The border width for the
#' title panels.}
#'
#' \item{\code{lwd.title=1}:}{ Integer scalar. The border width for the title
#' panels}
#'
#' \item{\code{lwd.grid=1}:}{ Numeric scalar. Default line width for grid
#' lines, both when \code{type=="g"} in \code{\linkS4class{DataTrack}}s and when
#' display parameter \code{grid==TRUE}.}
#'
#' \item{\code{reverseStrand=FALSE}:}{ Logical scalar. Set up the plotting
#' coordinates in 3' -> 5' direction if \code{TRUE}.  This will effectively
#' mirror the plot on the vertical axis.}
#'
#' \item{\code{rotation.title=90}:}{ 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.}
#'
#' \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.}
#'
#' }
#'
#' }
#'
#' \item{AlignmentsTrack:}{
#'
#' \describe{
#'
#' \item{\code{alpha.reads=0.5}:}{ Numeric scalar between 0 and 1. The
#' transparency of the individual read icons. Can be used to indicate
#' overlapping regions in read pairs. Only on supported devices.}
#'
#' \item{\code{alpha.mismatch=1}:}{ Numeric scalar between 0 and 1. The
#' transparency of the mismatch base information.}
#'
#' \item{\code{cex=0.7}:}{ Numeric Scalar. The global character expansion
#' factor.}
#'
#' \item{\code{cex.mismatch=NULL}:}{ Numeric Scalar. The character expansion
#' factor for the mismatch base letters.}
#'
#' \item{\code{col.coverage=NULL}:}{ Integer or character scalar.  The line
#' color for the coverage profile.}
#'
#' \item{\code{col.gap="#808080"}:}{ Integer or character scalar.  The color of
#' the line that is bridging the gap regions in gapped alignments.}
#'
#' \item{\code{col.mates="#E0E0E0"}:}{ Integer or character scalar.  The color
#' of the line that is connecting two paired reads.}
#'
#' \item{\code{col.deletion="#000000"}:}{ Integer or character scalar. The
#' color of the line that is bridging the deleted regions in alignments.}
#'
#' \item{\code{col.insertion="#984EA3"}:}{ Integer or character scalar. The
#' color of the line that highlighting insertions in alignments.}
#'
#' \item{\code{col.mismatch="#808080"}:}{ Integer or character scalar. The box
#' color around mismatch bases.}
#'
#' \item{\code{col.reads=NULL}:}{ Integer or character scalar.  The box color
#' around reads.}
#'
#' \item{\code{col.sashimi=NULL}:}{ Integer or character scalar.  The line
#' color for sashimi plots.}
#'
#' \item{\code{col="#808080"}:}{ Integer or character scalar. The default color
#' of all line elements.}
#'
#' \item{\code{collapse=FALSE}:}{ Logical scalar. Do not perform any collapsing
#' of overlapping elements. Currently not supported.}
#'
#' \item{\code{coverageHeight=0.1}:}{ Numeric scalar. The height of the
#' coverage region of the track. Can either be a value between 0 and 1 in which
#' case it is taken as a relative height, or a positive value greater 1 in
#' which case it is interpreted as pixels.}
#'
#' \item{\code{fill.coverage=NULL}:}{ Integer or character scalar.  The fill
#' color for the coverage profile.}
#'
#' \item{\code{fill.reads=NULL}:}{ Integer or character scalar.  The fill color
#' for the read icons.}
#'
#' \item{\code{fill="#BABABA"}:}{ Integer or character scalar.  The default
#' fill color of all plot elements.}
#'
#' \item{\code{fontface.mismatch=2}:}{ Integer scalar. The font face for
#' mismatch bases.}
#'
#' \item{\code{lty.coverage=NULL}:}{ Integer or character scalar.  The line
#' type of the coverage profile.}
#'
#' \item{\code{lty.gap=NULL}:}{ Integer or character scalar. The type of the
#' line that is bridging the gap regions in gapped alignments.}
#'
#' \item{\code{lty.mates=NULL}:}{ Integer or character scalar.  The type of the
#' line that is connecting two paired reads.}
#'
#' \item{\code{lty.deletion=NULL}:}{ Integer or character scalar.  The type of
#' the line that is bridging the deleted regions in alignments.}
#'
#' \item{\code{lty.insertion=NULL}:}{ Integer or character scalar.  The type of
#' the line that highlighting insertions in alignments.}
#'
#' \item{\code{lty.mismatch=NULL}:}{ Integer or character scalar.  The box line
#' type around mismatch bases.}
#'
#' \item{\code{lty.reads=NULL}:}{ Integer or character scalar.  The box line
#' type around mismatch reads.}
#'
#' \item{\code{lty=1}:}{ Integer or character scalar. The default type of all
#' line elements.}
#'
#' \item{\code{lwd.coverage=NULL}:}{ Integer or character scalar.  The line
#' width of the coverage profile.}
#'
#' \item{\code{lwd.gap=NULL}:}{ Integer scalar. The width of the line that is
#' bridging the gap regions in gapped alignments.}
#'
#' \item{\code{lwd.mates=NULL}:}{ Integer scalar. The width of the line that is
#' connecting two paired reads.}
#'
#' \item{\code{lwd.deletion=NULL}:}{ Integer scalar. The width of the line that
#' is bridging the deleted regions in alignments.}
#'
#' \item{\code{lwd.insertion=NULL}:}{ Integer scalar. The width of the line
#' that highlighting insertions in alignments.}
#'
#' \item{\code{lwd.mismatch=NULL}:}{ Integer scalar. The box line width around
#' mismatch bases.}
#'
#' \item{\code{lwd.reads=NULL}:}{ Integer scalar. The box line width around
#' reads.}
#'
#' \item{\code{lwd.sashimiMax=10}:}{ Integer scalar. The maximal width of the
#' line in sashimi plots.}
#'
#' \item{\code{lwd=1}:}{ Integer scalar. The default width of all line
#' elements.}
#'
#' \item{\code{max.height=10}:}{ Integer scalar. The maximum height of an
#' individual read in pixels. Can be used in combination with \code{min.height}
#' to control the read and stacking appearance.}
#'
#' \item{\code{min.height=5}:}{ Integer scalar. The minimum height of an
#' individual read in pixels. Can be used in combination with \code{max.height}
#' to control the read and stacking appearance.}
#'
#' \item{\code{minCoverageHeight=50}:}{ Integer scalar. The minimum height of
#' the coverage section. Uselful in combination with a relative setting of
#' \code{coverageHeight}.}
#'
#' \item{\code{minSashimiHeight=50}:}{ Integer scalar. The minimum height of
#' the sashimi section. Uselful in combination with a relative setting of
#' \code{sashimiHeight}.}
#'
#' \item{\code{noLetters=FALSE}:}{ Logical scalar. Always plot colored boxes
#' for mismatch bases regardles of the available space.}
#'
#' \item{\code{sashimiFilter=NULL}:}{ GRanges object. Only junctions which
#' overlap equally with \code{sashimiFilter} GRanges are shown. Default
#' \code{NULL}, no filtering.}
#'
#' \item{\code{sashimiFilterTolerance=0}:}{ Integer scalar. Only used in
#' combination with \code{sashimiFilter}. It allows to include junctions whose
#' starts/ends are within specified distance from \code{sashimiFilter} GRanges.
#' This is useful for cases where the aligner did not place the junction reads
#' precisely. Default \code{0L} , no tolerance.}
#'
#' \item{\code{sashimiHeight=0.1}:}{ Integer scalar. The height of the sashimi
#' part of the track. Can either be a value between 0 and 1 in which case it is
#' taken as a relative height, or a positive value greater 1 in which case it
#' is interpreted as pixels.}
#'
#' \item{\code{sashimiScore=1}:}{ Integer scalar. The minimum number of reads
#' supporting the junction.}
#'
#' \item{\code{sashimiStrand="*"}:}{ Integer scalar. Only reads which have the
#' specified strand are considered to count the junctions.}
#'
#' \item{\code{sashimiTransformation=NULL}:}{ Function. Applied to the junction
#' score vector prior to plotting. The function should accept exactly one input
#' argument and its return value needs to be a numeric vector of identical
#' length as the input data.}
#'
#' \item{\code{showIndels=FALSE}:}{ Logical scalar. Consider insertions and
#' deletions in coverage and pile-up. Default is \code{FALSE}. If set to
#' \code{TRUE} the deletions defined in CIGAR string are not considered in
#' coverage plot. The deletions are displayed as bridging lines in pile-up
#' track. Insertions are shown as vertical bars.}
#'
#' \item{\code{showMismatches=TRUE}:}{ Logical scalar. Add mismatch
#' information, either as individual base letters or using color coded bars.
#' This implies that the reference sequence has been provided, either to the
#' class constructor or as part of the track list.}
#'
#' \item{\code{size=NULL}:}{ Numeric scalar. The size of the track.  Defaults
#' to automatic sizing.}
#'
#' \item{\code{transformation=NULL}:}{ Function. Applied to the coverage vector
#' prior to plotting. The function should accept exactly one input argument and
#' its return value needs to be a numeric Rle of identical length as the input
#' data.}
#'
#' \item{\code{type=c("coverage", "pileup")}:}{ Character vactor.  The type of
#' information to plot. For \code{coverage} a coverage plot, potentially
#' augmented by base mismatch information, for \code{sashimi} a sashimi plot,
#' showing the juctions, and for \code{pileup} the pileups of the individual
#' reads. These three can be combined.}
#'
#' }
#'
#' \bold{\emph{Inherited from class StackedTrack:}}
#'
#' \describe{
#'
#' \item{\code{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.}
#'
#' \item{\code{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.}
#'
#' }
#'
#' \bold{\emph{Inherited from class GdObject:}}
#'
#' \describe{
#'
#' \item{\code{alpha=1}:}{ Numeric scalar. The transparency for all track
#' items.}
#'
#' \item{\code{alpha.title=NULL}:}{ Numeric scalar. The transparency for the
#' title panel.}
#'
#' \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 panel.}
#'
#' \item{\code{background.legend="transparent"}:}{ Integer or character scalar.
#' The background color for the legend.}
#'
#' \item{\code{cex.axis=NULL}:}{ Numeric scalar. The expansion factor for the
#' axis annotation. Defaults to \code{NULL}, in which case it is automatically
#' determined 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.border.title="white"}:}{ Integer or character scalar. The
#' border color for the title panels.}
#'
#' \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{\linkS4class{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 border
#' color for the title panels}
#'
#' \item{\code{fontcolor="black"}:}{ Integer or character scalar.  The font
#' color for all text, unless a more specific definition exists.}
#'
#' \item{\code{fontface.title=2}:}{ Integer or character scalar.  The font face
#' for the title panels.}
#'
#' \item{\code{fontface=1}:}{ Integer or character scalar. The font face for
#' all text, unless a more specific definition exists.}
#'
#' \item{\code{fontfamily.title="sans"}:}{ Integer or character scalar. The
#' font family for the title panels.}
#'
#' \item{\code{fontfamily="sans"}:}{ Integer or character scalar.  The font
#' family for all text, unless a more specific definition exists.}
#'
#' \item{\code{fontsize=12}:}{ Numeric scalar. The font size for all text,
#' unless a more specific definition exists.}
#'
#' \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{lineheight=1}:}{ Numeric scalar. The font line height for all
#' text, unless a more specific definition exists.}
#'
#' \item{\code{lty.grid="solid"}:}{ Integer or character scalar.  Default line
#' type for grid lines, both when \code{type=="g"} in \code{\linkS4class{DataTrack}}s
#' and when display parameter \code{grid==TRUE}.}
#'
#' \item{\code{lwd.border.title=1}:}{ Integer scalar. The border width for the
#' title panels.}
#'
#' \item{\code{lwd.title=1}:}{ Integer scalar. The border width for the title
#' panels}
#'
#' \item{\code{lwd.grid=1}:}{ Numeric scalar. Default line width for grid
#' lines, both when \code{type=="g"} in \code{\linkS4class{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.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{reverseStrand=FALSE}:}{ Logical scalar. Set up the plotting
#' coordinates in 3' -> 5' direction if \code{TRUE}.  This will effectively
#' mirror the plot on the vertical axis.}
#'
#' \item{\code{rotation.title=90}:}{ 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.}
#'
#' \item{\code{rotation=0}:}{ The rotation angle for all text unless a more
#' specific definiton exists.}
#'
#' \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.}
#'
#' }
#'
#' }
#'
#' }
#'
#' @name settings
#'
#' @author Florian Hahne
#'
#' @seealso
#' \code{\linkS4class{AnnotationTrack}}
#'
#' \code{\linkS4class{DataTrack}}
#'
#' \code{\linkS4class{DisplayPars}}
#'
#' \code{\linkS4class{GdObject}}
#'
#' \code{\link{availableDisplayPars}}
#'
#' \code{\link{collapsing}}
#'
#' \code{\link{grouping}}
#'
#' \code{\link{horizonplot}}
#'
#' \code{\link{panel.bwplot}}
#'
#' \code{\link{panel.grid}}
#'
#' \code{\link{panel.loess}}
#'
#' \code{\link{panel.xyplot}}
#'
#' \code{\link{plotTracks}}
#'
#' @examples
#'
#' ## Which scheme is used?
#' getOption("Gviz.scheme")
#'
#' ## Change default settings for GeneRegionTrack
#' scheme <- getScheme()
#' scheme$GeneRegionTrack$fill <- "salmon"
#' scheme$GeneRegionTrack$col <- NULL
#' scheme$GeneRegionTrack$transcriptAnnotation <- "transcript"
#'
#' ## replace default scheme with myScheme
#' addScheme(scheme, "myScheme")
#' options(Gviz.scheme = "myScheme")
#' getOption("Gviz.scheme")
#'
#' data(geneModels)
#' grtrack <- GeneRegionTrack(geneModels, genome = "hg19", chromosome = "chr7", name = "Gene Model")
#' plotTracks(grtrack)
NULL