\name{settings} \Rdversion{1.1} \alias{settings} \title{Setting display parameters to control the look and feel of the plots} \description{ 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. } \details{ 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{\link{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. } \section{Display Parameters}{ \describe{ \item{GenomeAxisTrack}{: \describe{ \item{}{\code{cex.id=0.7}: Numeric scalar. The text size for the optional range annotation.} \item{}{\code{fontsize=10}: Numeric scalar. Font size for the axis annotation text in points.} \item{}{\code{background.title="transparent"}: Character scalar. The background color for the title panel. Defaults to omit the background.} \item{}{\code{fontcolor="#808080"}: Character scalar. The font color for the axis annotation text.} \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{lwd=2}: Numeric scalar. The line width for the axis elementes.} \item{}{\code{add35=FALSE}: Logical scalar. Add 3' to 5' direction indicators.} \item{}{\code{showTitle=FALSE}: Logical scalar. Plot a title panel. Defaults to omit the title panel.} \item{}{\code{add53=FALSE}: Logical scalar. Add 5' to 3' direction indicators.} \item{}{\code{littleTicks=FALSE}: Logical scalar. Add more fine-grained tick marks.} \item{}{\code{distFromAxis=1}: Numeric scalar. Control the distance of the axis annotation from the tick marks.} \item{}{\code{col.id="white"}: Character scalar. The text color for the optional range annotation.} \item{}{\code{labelPos="alternating"}: Character vector, one in "alternating", "revAlternating", "above" or "below". The vertical positioning of the axis labels.} \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{cex=0.8}: Numeric scalar. The overall font expansion factor for the axis annotation text.} \item{}{\code{fill.range="cornsilk3"}: Character scalar. The fill color for highlighted regions on the axis.} \item{}{\code{showId=FALSE}: Logical scalar. Show the optional range highlighting annotation.} \item{}{\code{col.range="cornsilk4"}: Character scalar. The border color for highlighted regions on the axis.} \item{}{\code{col="darkgray"}: Character scalar. The color for the axis lines and tickmarks.} } \bold{\emph{Inherited from class GdObject:}} \describe{ \item{}{\code{fontface=1}: Integer or character scalar. The font face for all text.} \item{}{\code{h=-1}: Integer scalar. Parameter controlling the number of horizontal grid lines, see \code{\link{panel.grid}} for details.} \item{}{\code{col.axis="white"}: Integer or character scalar. The font and line color for the y axis, if any.} \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting of a grid.} \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{alpha=1}: Numeric scalar. The transparency for all track items.} \item{}{\code{col.grid="#808080"}: Integer or character scalar. Default line color for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{lty="solid"}: Numeric scalar. Default line type setting for all plotting elements, unless there is a more specific control defined elsewhere.} \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{background.panel="transparent"}: Integer or character scalar. The background color of the content panel.} \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{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{v=-1}: Integer scalar. Parameter controlling the number of vertical grid lines, see \code{\link{panel.grid}} for details.} \item{}{\code{collapse=TRUE}: Boolean controlling wether to collapse the content of the track to accomodate the minimum current device resolution. See \code{\link{collapsing}} for details.} \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion factor for the axis annotation. Defaults to \code{NULL}, in which case it is computed based on the available space.} \item{}{\code{fontface.title=2}: Integer or character scalar. The font face for the title panels.} \item{}{\code{lineheight=1}: Numeric scalar. The font line height for all text.} \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{lwd.grid=1}: Numeric scalar. Default line width for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{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.frame="lightgray"}: Integer or character scalar. The line color used for the panel frame, if \code{frame==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.} \item{}{\code{lty.grid="solid"}: Integer or character scalar. Default line type for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{col.title="white"}: Integer or character scalar. The font color for the title panels.} \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{showAxis=TRUE}: Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).} \item{}{\code{fontfamily="sans"}: Integer or character scalar. The font family for all text.} } } \item{DataTrack}{: \describe{ \item{}{\code{pch=20}: Integer scalar. The type of glyph used for plotting symbols.} \item{}{\code{notch=FALSE}: Logical scalar. Parameter controlling the boxplot appearance. See \code{\link{panel.bwplot}} for details.} \item{}{\code{cex=0.7}: Numeric scalar. The default pixel size for plotting symbols.} \item{}{\code{box.width=NULL}: Numeric scalar. Parameter controlling the boxplot appearance. See \code{\link{panel.bwplot}} 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{levels.fos=NULL}: Numeric scalar. Parameter controlling the boxplot appearance. See \code{\link{panel.bwplot}} for details.} \item{}{\code{gradient=c("#F7FBFF", "#DEEBF7", "#C6DBEF", "#9ECAE1", "#6BAED6", "#4292C6", "#2171B5", "#08519C", "#08306B")}: Character vector. The base colors for the 'gradient' plotting type.} \item{}{\code{min.distance=0}: Numeric scalar. The mimimum distance in pixel below which to collapse ranges.} \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{type="p"}: Character vector. The plot type, one or several in \code{c("p","l", "b", "a", "s", "g", "r", "S", "smooth", "histogram", "mountain", "h", "boxplot", "gradient", "heatmap")}. See 'Details' section in \code{\linkS4class{DataTrack}} for more information on the individual plotting types.} \item{}{\code{notch.frac=0.5}: Numeric scalar. Parameter controlling the boxplot appearance. See \code{\link{panel.bwplot}} for details.} \item{}{\code{ylim=NULL}: Numeric vector of length 2. The range of the y-axis scale.} \item{}{\code{fill.histogram="lightgray"}: Character scalar. Fill color in histogram-type plots, defaults to the setting of \code{fill}.} \item{}{\code{baseline=NULL}: Numeric scalar. Y-axis position of an optional baseline. This parameter has a special meaning for mountain-type plots, see the 'Details' section in \code{\linkS4class{DataTrack}} for more information.} \item{}{\code{collapse=FALSE}: Logical scalar. Collapse overlapping ranges and aggregate the underlying data.} \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{col.mountain=NULL}: Character scalar. Line color in mountain-type plots, defaults to the setting of \code{col}.} \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{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{box.ratio=1}: Numeric scalar. Parameter controlling the boxplot appearance. See \code{\link{panel.bwplot}} for details.} \item{}{\code{varwidth=FALSE}: Logical scalar. Parameter controlling the boxplot appearance. See \code{\link{panel.bwplot}} 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{separator=0}: Numeric scalar. Number of pixels used to separate individual samples in heatmap-type plots.} \item{}{\code{ncolor=100}: Integer scalar. The number of colors for the 'gradient' plotting type} \item{}{\code{stats=X[[44]]}: Function. Parameter controlling the boxplot appearance. See \code{\link{panel.bwplot}} for details.} \item{}{\code{amount=NULL}: Numeric scalar. Amount of jittering in xy-type plots. See \code{\link{panel.xyplot}} for details.} \item{}{\code{na.rm=FALSE}: Boolean controlling whether to discard all NA values when plotting or to keep empty spaces for NAs} \item{}{\code{lwd.baseline=NULL}: Numeric scalar. Line width of the optional baseline, defaults to the setting of \code{lwd}.} \item{}{\code{windowSize=NULL}: Numeric scalar. The size of the running window when the value of \code{window} is negative.} \item{}{\code{lty.mountain=NULL}: Character or numeric scalar. Line type in mountain-type plots, defaults to the setting of \code{lty}.} \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{groups=NULL}: Vector coercable to a factor. Optional sample grouping. See 'Details' section in \code{\linkS4class{DataTrack}} for further information.} \item{}{\code{lty.baseline=NULL}: Character or numeric scalar. Line type of the optional baseline, defaults to the setting of \code{lty}.} \item{}{\code{col.baseline=NULL}: Character scalar. Color for the optional baseline, defaults to the setting of \code{col}.} \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{fill.mountain=c("#CCFFFF", "#FFCCFF")}: Character vector of length 2. Fill color in mountain-type plots.} \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{do.out=TRUE}: Logical scalar. Parameter controlling the boxplot appearance. See \code{\link{panel.bwplot}} for details.} \item{}{\code{col.histogram="#808080"}: Character scalar. Line color in histogram-type plots.} \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{coef=1.5}: Numeric scalar. Parameter controlling the boxplot appearance. See \code{\link{panel.bwplot}} for details.} \item{}{\code{lwd.mountain=NULL}: Numeric scalar. Line width in mountain-type plots, defaults to the setting of \code{lwd}.} \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.} } \bold{\emph{Inherited from class GdObject:}} \describe{ \item{}{\code{fontface=1}: Integer or character scalar. The font face for all text.} \item{}{\code{fontsize=12}: Numeric scalar. The font size for all text.} \item{}{\code{h=-1}: Integer scalar. Parameter controlling the number of horizontal grid lines, see \code{\link{panel.grid}} for details.} \item{}{\code{fontcolor="black"}: Integer or character scalar. The font color for all text.} \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{col.axis="white"}: Integer or character scalar. The font and line color for the y axis, if any.} \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting of a grid.} \item{}{\code{fontfamily.title="sans"}: Integer or character scalar. The font family for the title panels.} \item{}{\code{background.title="lightgray"}: Integer or character scalar. The background color for the title panels.} \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the track when plotting.} \item{}{\code{alpha=1}: Numeric scalar. The transparency for all track items.} \item{}{\code{col.grid="#808080"}: Integer or character scalar. Default line color for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{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{lty="solid"}: Numeric scalar. Default line type setting for all plotting elements, unless there is a more specific control defined elsewhere.} \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{background.panel="transparent"}: Integer or character scalar. The background color of the content panel.} \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{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{v=-1}: Integer scalar. Parameter controlling the number of vertical grid lines, see \code{\link{panel.grid}} for details.} \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion factor for the axis annotation. Defaults to \code{NULL}, in which case it is computed based on the available space.} \item{}{\code{fontface.title=2}: Integer or character scalar. The font face for the title panels.} \item{}{\code{lineheight=1}: Numeric scalar. The font line height for all text.} \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{lwd.grid=1}: Numeric scalar. Default line width for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{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.frame="lightgray"}: Integer or character scalar. The line color used for the panel frame, if \code{frame==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.} \item{}{\code{col="#0080FF"}: Integer or character scalar. Default line color setting for all plotting elements, unless there is a more specific control defined elsewhere.} \item{}{\code{lty.grid="solid"}: Integer or character scalar. Default line type for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{col.title="white"}: Integer or character scalar. The font color for the title panels.} \item{}{\code{showAxis=TRUE}: Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).} \item{}{\code{fontfamily="sans"}: Integer or character scalar. The font family for all text.} } } \item{IdeogramTrack}{: \describe{ \item{}{\code{fontsize=10}: Numeric scalar. The font size for the chromosome name text.} \item{}{\code{background.title="transparent"}: Character scalar. The background color for the title panel. Defaults to omit the background.} \item{}{\code{fontcolor="#808080"}: Character scalar. The font color for the chromosome name text.} \item{}{\code{size=NULL}: Numeric scalar. The relative size of the track. Defaults to automatic size setting. Can be overridden in the \code{\link{plotTracks}} function.} \item{}{\code{showTitle=FALSE}: Logical scalar. Plot a title panel. Defaults to omit the title panel.} \item{}{\code{cex=0.8}: Numeric scalar. The overall font expansion factor for the chromosome name text.} \item{}{\code{fill="#FFE3E6"}: Character scalar. The fill color 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{col="red"}: Character scalar. The border color used for the highlighting of the currently displayed genomic region.} \item{}{\code{bevel=0.45}: Numeric scalar, between 0 and 1. The level of smoothness for the two ends of the ideogram.} } \bold{\emph{Inherited from class GdObject:}} \describe{ \item{}{\code{fontface=1}: Integer or character scalar. The font face for all text.} \item{}{\code{h=-1}: Integer scalar. Parameter controlling the number of horizontal grid lines, see \code{\link{panel.grid}} for details.} \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{col.axis="white"}: Integer or character scalar. The font and line color for the y axis, if any.} \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting of a grid.} \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{alpha=1}: Numeric scalar. The transparency for all track items.} \item{}{\code{col.grid="#808080"}: Integer or character scalar. Default line color for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{lty="solid"}: Numeric scalar. Default line type setting for all plotting elements, unless there is a more specific control defined elsewhere.} \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{background.panel="transparent"}: Integer or character scalar. The background color of the content panel.} \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{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{v=-1}: Integer scalar. Parameter controlling the number of vertical grid lines, see \code{\link{panel.grid}} for details.} \item{}{\code{collapse=TRUE}: Boolean controlling wether to collapse the content of the track to accomodate the minimum current device resolution. See \code{\link{collapsing}} for details.} \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion factor for the axis annotation. Defaults to \code{NULL}, in which case it is computed based on the available space.} \item{}{\code{fontface.title=2}: Integer or character scalar. The font face for the title panels.} \item{}{\code{lineheight=1}: Numeric scalar. The font line height for all text.} \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{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.frame="lightgray"}: Integer or character scalar. The line color used for the panel frame, if \code{frame==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.} \item{}{\code{lty.grid="solid"}: Integer or character scalar. Default line type for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{col.title="white"}: Integer or character scalar. The font color for the title panels.} \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{showAxis=TRUE}: Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).} \item{}{\code{fontfamily="sans"}: Integer or character scalar. The font family for all text.} } } \item{AnnotationTrack}{: \describe{ \item{}{\code{fontface.group=2}: Numeric scalar. The font face for the group-level annotation.} \item{}{\code{showFeatureId=FALSE}: Logical scalar. Control whether to plot the individual track item identifiers.} \item{}{\code{fontsize=12}: Numeric scalar. The font size for item identifiers.} \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{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{fontcolor="white"}: Character or integer scalar. The font color for item identifiers.} \item{}{\code{fontfamily="sans"}: Character scalar. The font family for item identifiers.} \item{}{\code{size=1}: Numeric scalar. The relative size of the track. Can be overridden in the \code{\link{plotTracks}} function.} \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{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{shape="arrow"}: Character scalar. The shape in which to display the track items. Currently only \code{box}, \code{arrow}, \code{ellipse}, and \code{smallArrow} are implemented.} \item{}{\code{cex=1}: Numeric scalar. The font expansion factor for item identifiers.} \item{}{\code{fontface=1}: Integer scalar. The font face for item identifiers.} \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{showId=FALSE}: Logical scalar. Control whether to annotate individual groups.} \item{}{\code{cex.group=0.6}: Numeric scalar. The font expansion factor for the group-level annotation.} \item{}{\code{lineheight=1}: Numeric scalar. The font line height for item identifiers.} \item{}{\code{fontcolor.group="#808080"}: Character or integer scalar. The font color for the group-level annotation.} \item{}{\code{col="transparent"}: Character or integer scalar. The border color for all track items.} \item{}{\code{rotation=0}: Numeric scalar. The degree of text rotation for item identifiers.} } \bold{\emph{Inherited from class GdObject:}} \describe{ \item{}{\code{h=-1}: Integer scalar. Parameter controlling the number of horizontal grid lines, see \code{\link{panel.grid}} for details.} \item{}{\code{col.axis="white"}: Integer or character scalar. The font and line color for the y axis, if any.} \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting of a grid.} \item{}{\code{fontfamily.title="sans"}: Integer or character scalar. The font family for the title panels.} \item{}{\code{background.title="lightgray"}: Integer or character scalar. The background color for the title panels.} \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the track when plotting.} \item{}{\code{alpha=1}: Numeric scalar. The transparency for all track items.} \item{}{\code{col.grid="#808080"}: Integer or character scalar. Default line color for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{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{col.line=NULL}: Integer or character scalar. Default colors for plot lines. Usually the same as the global \code{col} parameter.} \item{}{\code{background.panel="transparent"}: Integer or character scalar. The background color of the content panel.} \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{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{v=-1}: Integer scalar. Parameter controlling the number of vertical grid lines, see \code{\link{panel.grid}} for details.} \item{}{\code{collapse=TRUE}: Boolean controlling wether to collapse the content of the track to accomodate the minimum current device resolution. See \code{\link{collapsing}} for details.} \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion factor for the axis annotation. Defaults to \code{NULL}, in which case it is computed based on the available space.} \item{}{\code{fontface.title=2}: Integer or character scalar. The font face for the title panels.} \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{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.frame="lightgray"}: Integer or character scalar. The line color used for the panel frame, if \code{frame==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.} \item{}{\code{lty.grid="solid"}: Integer or character scalar. Default line type for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{col.title="white"}: Integer or character scalar. The font color for the title panels.} \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{showAxis=TRUE}: Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).} } } \item{GeneRegionTrack}{: \describe{ \item{}{\code{showExonId=FALSE}: Logical scalar. Control whether to plot the individual exon identifiers.} \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{geneSymbols=TRUE}: Logical scalar. Use human-readable gene symbols or gene IDs for the transcript annotation.} \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.} } \bold{\emph{Inherited from class AnnotationTrack:}} \describe{ \item{}{\code{fontface.group=2}: Numeric scalar. The font face for the group-level annotation.} \item{}{\code{showFeatureId=FALSE}: Logical scalar. Control whether to plot the individual track item identifiers.} \item{}{\code{fontsize=12}: Numeric scalar. The font size for item identifiers.} \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{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{fontcolor="white"}: Character or integer scalar. The font color for item identifiers.} \item{}{\code{fontfamily="sans"}: Character scalar. The font family for item identifiers.} \item{}{\code{size=1}: Numeric scalar. The relative size of the track. Can be overridden in the \code{\link{plotTracks}} function.} \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{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{cex=1}: Numeric scalar. The font expansion factor for item identifiers.} \item{}{\code{fontface=1}: Integer scalar. The font face for item identifiers.} \item{}{\code{showId=FALSE}: Logical scalar. Control whether to annotate individual groups.} \item{}{\code{cex.group=0.6}: Numeric scalar. The font expansion factor for the group-level annotation.} \item{}{\code{lineheight=1}: Numeric scalar. The font line height for item identifiers.} \item{}{\code{fontcolor.group="#808080"}: Character or integer scalar. The font color for the group-level annotation.} \item{}{\code{col="transparent"}: Character or integer scalar. The border color for all track items.} \item{}{\code{rotation=0}: Numeric scalar. The degree of text rotation for item identifiers.} } \bold{\emph{Inherited from class GdObject:}} \describe{ \item{}{\code{h=-1}: Integer scalar. Parameter controlling the number of horizontal grid lines, see \code{\link{panel.grid}} for details.} \item{}{\code{col.axis="white"}: Integer or character scalar. The font and line color for the y axis, if any.} \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting of a grid.} \item{}{\code{fontfamily.title="sans"}: Integer or character scalar. The font family for the title panels.} \item{}{\code{background.title="lightgray"}: Integer or character scalar. The background color for the title panels.} \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the track when plotting.} \item{}{\code{alpha=1}: Numeric scalar. The transparency for all track items.} \item{}{\code{col.grid="#808080"}: Integer or character scalar. Default line color for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{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{col.line=NULL}: Integer or character scalar. Default colors for plot lines. Usually the same as the global \code{col} parameter.} \item{}{\code{background.panel="transparent"}: Integer or character scalar. The background color of the content panel.} \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{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{v=-1}: Integer scalar. Parameter controlling the number of vertical grid lines, see \code{\link{panel.grid}} for details.} \item{}{\code{collapse=TRUE}: Boolean controlling wether to collapse the content of the track to accomodate the minimum current device resolution. See \code{\link{collapsing}} for details.} \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion factor for the axis annotation. Defaults to \code{NULL}, in which case it is computed based on the available space.} \item{}{\code{fontface.title=2}: Integer or character scalar. The font face for the title panels.} \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{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.frame="lightgray"}: Integer or character scalar. The line color used for the panel frame, if \code{frame==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.} \item{}{\code{lty.grid="solid"}: Integer or character scalar. Default line type for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{col.title="white"}: Integer or character scalar. The font color for the title panels.} \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{showAxis=TRUE}: Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).} } } \item{BiomartGeneRegionTrack}{: \describe{ \item{}{\code{scRNA_pseudogene="darkorange2"}: Character or integer scalar. Fill color for annotation objects of type 'scRNA_pseudogene'.} \item{}{\code{miRNA_pseudogene="cornsilk"}: Character or integer scalar. Fill color for annotation objects of type 'miRNA_pseudogene'.} \item{}{\code{D_segment="lightblue"}: Character or integer scalar. Fill color for annotation objects of type 'C_segment'.} \item{}{\code{scRNA="darkorange"}: Character or integer scalar. Fill color for annotation objects of type 'scRNA'.} \item{}{\code{J_segment="dodgerblue2"}: Character or integer scalar. Fill color for annotation objects of type 'C_segment'.} \item{}{\code{Mt_tRNA_pseudogene="darkgoldenrod1"}: Character or integer scalar. Fill color for annotation objects of type 'Mt_tRNA_pseudogene'.} \item{}{\code{Mt_rRNA="yellow"}: Character or integer scalar. Fill color for annotation objects of type 'Mt_rRNA'.} \item{}{\code{tRNA_pseudogene="antiquewhite3"}: Character or integer scalar. Fill color for annotation objects of type 'tRNA_pseudogene'.} \item{}{\code{rRNA_pseudogene="darkolivegreen"}: Character or integer scalar. Fill color for annotation objects of type 'rRNA_pseudogene'.} \item{}{\code{miRNA="cornflowerblue"}: Character or integer scalar. Fill color for annotation objects of type 'L_segment'.} \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{protein_coding="gold4"}: Character or integer scalar. Fill color for annotation objects of type 'protein_coding'.} \item{}{\code{Mt_tRNA="darkgoldenrod"}: Character or integer scalar. Fill color for annotation objects of type 'Mt_tRNA'.} \item{}{\code{retrotransposed="blueviolet"}: Character or integer scalar. Fill color for annotation objects of type 'retrotransposed'.} \item{}{\code{snRNA="coral"}: Character or integer scalar. Fill color for annotation objects of type 'snRNA'.} \item{}{\code{V_segment="aquamarine"}: Character or integer scalar. Fill color for annotation objects of type 'V_segment'.} \item{}{\code{snRNA_pseudogene="coral3"}: Character or integer scalar. Fill color for annotation objects of type 'snRNA_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{snoRNA_pseudogene="cyan2"}: Character or integer scalar. Fill color for annotation objects of type 'snoRNA_pseudogene'.} \item{}{\code{snoRNA="cyan"}: Character or integer scalar. Fill color for annotation objects of type 'snoRNA'.} \item{}{\code{C_segment="burlywood4"}: Character or integer scalar. Fill color for annotation objects of type 'C_segment'.} } \bold{\emph{Inherited from class GeneRegionTrack:}} \describe{ \item{}{\code{showExonId=FALSE}: Logical scalar. Control whether to plot the individual exon identifiers.} \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{geneSymbols=TRUE}: Logical scalar. Use human-readable gene symbols or gene IDs for the transcript annotation.} \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.} } \bold{\emph{Inherited from class AnnotationTrack:}} \describe{ \item{}{\code{fontface.group=2}: Numeric scalar. The font face for the group-level annotation.} \item{}{\code{showFeatureId=FALSE}: Logical scalar. Control whether to plot the individual track item identifiers.} \item{}{\code{fontsize=12}: Numeric scalar. The font size for item identifiers.} \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{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{fontcolor="white"}: Character or integer scalar. The font color for item identifiers.} \item{}{\code{fontfamily="sans"}: Character scalar. The font family for item identifiers.} \item{}{\code{size=1}: Numeric scalar. The relative size of the track. Can be overridden in the \code{\link{plotTracks}} function.} \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{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{cex=1}: Numeric scalar. The font expansion factor for item identifiers.} \item{}{\code{fontface=1}: Integer scalar. The font face for item identifiers.} \item{}{\code{showId=FALSE}: Logical scalar. Control whether to annotate individual groups.} \item{}{\code{cex.group=0.6}: Numeric scalar. The font expansion factor for the group-level annotation.} \item{}{\code{lineheight=1}: Numeric scalar. The font line height for item identifiers.} \item{}{\code{fontcolor.group="#808080"}: Character or integer scalar. The font color for the group-level annotation.} \item{}{\code{col="transparent"}: Character or integer scalar. The border color for all track items.} \item{}{\code{rotation=0}: Numeric scalar. The degree of text rotation for item identifiers.} } \bold{\emph{Inherited from class GdObject:}} \describe{ \item{}{\code{h=-1}: Integer scalar. Parameter controlling the number of horizontal grid lines, see \code{\link{panel.grid}} for details.} \item{}{\code{col.axis="white"}: Integer or character scalar. The font and line color for the y axis, if any.} \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting of a grid.} \item{}{\code{fontfamily.title="sans"}: Integer or character scalar. The font family for the title panels.} \item{}{\code{background.title="lightgray"}: Integer or character scalar. The background color for the title panels.} \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the track when plotting.} \item{}{\code{alpha=1}: Numeric scalar. The transparency for all track items.} \item{}{\code{col.grid="#808080"}: Integer or character scalar. Default line color for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{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{col.line=NULL}: Integer or character scalar. Default colors for plot lines. Usually the same as the global \code{col} parameter.} \item{}{\code{background.panel="transparent"}: Integer or character scalar. The background color of the content panel.} \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{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{v=-1}: Integer scalar. Parameter controlling the number of vertical grid lines, see \code{\link{panel.grid}} for details.} \item{}{\code{collapse=TRUE}: Boolean controlling wether to collapse the content of the track to accomodate the minimum current device resolution. See \code{\link{collapsing}} for details.} \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion factor for the axis annotation. Defaults to \code{NULL}, in which case it is computed based on the available space.} \item{}{\code{fontface.title=2}: Integer or character scalar. The font face for the title panels.} \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{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.frame="lightgray"}: Integer or character scalar. The line color used for the panel frame, if \code{frame==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.} \item{}{\code{lty.grid="solid"}: Integer or character scalar. Default line type for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{col.title="white"}: Integer or character scalar. The font color for the title panels.} \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{showAxis=TRUE}: Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).} } } \item{AlignedReadTrack}{: \describe{ \item{}{\code{detail="coverage"}: the amount of detail to plot the data. Either \code{coverage} to show the coverage only, or \code{reads} to show individual reads. For large data sets the latter can be very inefficient. Please note that \code{reads} is only available when the object has been created with option \code{coverageOnly=FALSE}.} \item{}{\code{type="histogram"}: the plot type, one or several in \code{c("p","l", "b", "a", "s", "g", "r", "S", "smooth", "histogram", "mountain", "h", "boxplot", "gradient", "heatmap")}. See the 'Details' section in \code{\linkS4class{DataTrack}} for more information on the individual plotting types.} \item{}{\code{size=NULL}: the relative size of the track. Defaults to size selection based on the underlying data. Can be overridden in the \code{\link{plotTracks}} function.} \item{}{\code{collapse=FALSE}: collapse overlapping ranges and aggregate the underlying data.} \item{}{\code{fill="#0080ff"}: the fill color for the coverage indicator.} } \bold{\emph{Inherited from class GdObject:}} \describe{ \item{}{\code{fontface=1}: Integer or character scalar. The font face for all text.} \item{}{\code{fontsize=12}: Numeric scalar. The font size for all text.} \item{}{\code{h=-1}: Integer scalar. Parameter controlling the number of horizontal grid lines, see \code{\link{panel.grid}} for details.} \item{}{\code{fontcolor="black"}: Integer or character scalar. The font color for all text.} \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{col.axis="white"}: Integer or character scalar. The font and line color for the y axis, if any.} \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting of a grid.} \item{}{\code{fontfamily.title="sans"}: Integer or character scalar. The font family for the title panels.} \item{}{\code{background.title="lightgray"}: Integer or character scalar. The background color for the title panels.} \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the track when plotting.} \item{}{\code{alpha=1}: Numeric scalar. The transparency for all track items.} \item{}{\code{col.grid="#808080"}: Integer or character scalar. Default line color for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{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{lty="solid"}: Numeric scalar. Default line type setting for all plotting elements, unless there is a more specific control defined elsewhere.} \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{background.panel="transparent"}: Integer or character scalar. The background color of the content panel.} \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{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{cex=1}: Numeric scalar. The overall font expansion factor for all text.} \item{}{\code{v=-1}: Integer scalar. Parameter controlling the number of vertical grid lines, see \code{\link{panel.grid}} for details.} \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion factor for the axis annotation. Defaults to \code{NULL}, in which case it is computed based on the available space.} \item{}{\code{fontface.title=2}: Integer or character scalar. The font face for the title panels.} \item{}{\code{lineheight=1}: Numeric scalar. The font line height for all text.} \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{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.frame="lightgray"}: Integer or character scalar. The line color used for the panel frame, if \code{frame==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.} \item{}{\code{col="#0080FF"}: Integer or character scalar. Default line color setting for all plotting elements, unless there is a more specific control defined elsewhere.} \item{}{\code{lty.grid="solid"}: Integer or character scalar. Default line type for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s and when display parameter \code{grid==TRUE}.} \item{}{\code{col.title="white"}: Integer or character scalar. The font color for the title panels.} \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{showAxis=TRUE}: Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).} \item{}{\code{fontfamily="sans"}: Integer or character scalar. The font family for all text.} } } } } \author{ Florian Hahne } \seealso{ \code{\linkS4class{AnnotationTrack}} \code{\linkS4class{DataTrack}} \code{\linkS4class{DisplayPars}} \code{\linkS4class{GdObject}} \code{\link{availableDisplayPars}} \code{\link{collapsing}} \code{\link{displayPars}} \code{\link{grouping}} \code{\link{panel.bwplot}} \code{\link{panel.grid}} \code{\link{panel.loess}} \code{\link{panel.xyplot}} \code{\link{plotTracks}} }