man-roxygen/DisplayParams_param_old.R

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

#' ## Display Parameters

#' The following display parameters are set for objects of class `GdObject`
#' upon instantiation, unless one or more of them have already been set by
#' one of the optional sub-class initializers, which always get precedence
#' over these global defaults. See `settings` for details on setting
#' graphical parameters for tracks.


#' @param alpha=1 Numeric scalar. The transparency for all track items.
#' @param alpha.title=NULL Numeric scalar. The transparency for the title panel.
#' @param background.legend="transparent" Integer or character scalar.
#' The background colour for the legend.
#' @param background.panel="transparent" Integer or character scalar.
#' The background colour of the content panel.
#' @param background.title="lightgray" Integer or character scalar.
#' The background colour for the title panel.
#' @param cex=1 Numeric scalar. The overall font expansion factor for all text
#' and glyphs, unless a more specific definition exists.
#' @param cex.axis=NULL Numeric scalar. The expansion factor for the axis
#' annotation. Defaults to `NULL`, in which case it is automatically determined
#'  based on the available space.
#' @param cex.title=NULL Numeric scalar. The expansion factor for the title
#' panel. This effects the font size of both the title and the axis, if any.
#'  Defaults to NULL, which means that the text size is automatically adjusted
#'   to the available space.
#' @param col="#0080FF" Integer or character scalar. Default line colour setting
#' for all plotting elements, unless there is a more specific control defined
#' elsewhere.
#' @param col.axis="white" Integer or character scalar. The font and line colour
#' for the y axis, if any.
#' @param col.border.title="white" Integer or character scalar. The border
#' colour for the title panels.
#' @param col.frame="lightgray" Integer or character scalar. The line colour
#' used for the panel frame, if `frame==TRUE`
#' @param col.grid="#808080" Integer or character scalar. Default line colour
#' for grid lines, both when `type=="g"` in `DataTrack`s and when display
#' parameter `grid==TRUE`.
#' @param col.line=NULL Integer or character scalar. Default colours for plot
#'  lines. Usually the same as the global col parameter.
#' @param col.symbol=NULL Integer or character scalar. Default colours for plot
#' symbols. Usually the same as the global col parameter.
#' @param col.title="white" (Aliases `fontcolour.title`) Integer or character
#' scalar. The border colour for the title panels
#' @param collapse=TRUE Boolean controlling whether to collapse the content of
#' the track to accommodate the minimum current device resolution.
#' See collapsing for details.
#' @param fill="lightgray" Integer or character scalar. Default fill colour
#' setting for all plotting elements, unless there is a more specific control
#' defined elsewhere.
#' @param fontcolour="black" Integer or character scalar. The font colour for
#' all text, unless a more specific definition exists.
#' @param fontface=1 Integer or character scalar. The font face for all text,
#' unless a more specific definition exists.
#' @param fontface.title=2 Integer or character scalar. The font face for the
#' title panels.
#' @param fontfamily="sans" Integer or character scalar. The font family for all
#' text, unless a more specific definition exists.
#' @param fontfamily.title="sans" Integer or character scalar. The font family
#' for the title panels.
#' @param fontsize=12 Numeric scalar. The font size for all text, unless a more
#'  specific definition exists.
#' @param frame=FALSE Boolean. Draw a frame around the track when plotting.
#' @param grid=FALSE Boolean, switching on/off the plotting of a grid.
#' @param h=-1 Integer scalar. Parameter controlling the number of horizontal
#' grid lines, see panel.grid for details.
#' @param lineheight=1 Numeric scalar. The font line height for all text, unless
#'  a more specific definition exists.
#' @param lty="solid" Numeric scalar. Default line type setting for all plotting
#' elements, unless there is a more specific control defined elsewhere.
#' @param lty.grid="solid" Integer or character scalar. Default line type for
#'  grid lines, both when `type=="g"` in `DataTrack`s and when display parameter
#'  `grid==TRUE`.
#' @param lwd=1 Numeric scalar. Default line width setting for all plotting
#'  elements, unless there is a more specific control defined elsewhere.
#' @param lwd.border.title=1 Integer scalar. The border width for the title
#' panels.
#' @param lwd.grid=1 Numeric scalar. Default line width for grid lines, both
#' when `type=="g"` in `DataTrack`s and when display parameter `grid==TRUE`.
#' @param lwd.title=1 Integer scalar. The border width for the title panels
#' @param min.distance=1 Numeric scalar. The minimum pixel distance before
#' collapsing range items, only if `collapse==TRUE`. See collapsing for details.
#' @param min.height=3 Numeric scalar. The minimum range height in pixels to
#' display. All ranges are expanded to this size in order to avoid rendering
#'  issues. See collapsing for details.
#' @param min.width=1 Numeric scalar. The minimum range width in pixels to
#' display. All ranges are expanded to this size in order to avoid rendering
#' issues. See collapsing for details.
#' @param reverseStrand=FALSE Logical scalar. Set up the plotting coordinates
#'  in 3' -> 5' direction if `TRUE.` This will effectively mirror the plot
#'   on the vertical axis.
#' @param rotation=0 The rotation angle for all text unless a more specific
#' definition exists.
#' @param rotation.title=90 (Aliases rotation.title) The rotation angle for
#' the text in the title panel. Even though this can be adjusted, the automatic
#'  resizing of the title panel will currently not work, so use at own risk.
#' @param showAxis=TRUE Boolean controlling whether to plot a y axis (only
#' applies to track types where axes are implemented).
#' @param showTitle=TRUE Boolean controlling whether to plot a title panel.
#'  Although this can be set individually for each track, in multi-track plots
#'  as created by `plotTracks` there will still be an empty place holder in case
#'  any of the other tracks include a title. The same holds true for axes. Note
#'  that the the title panel background colour could be set to transparent in
#'  order to completely hide it.
#' @param size=1 Numeric scalar. The relative size of the track. Can be
#' overridden in the `plotTracks` function.
#' @param v=-1 Integer scalar. Parameter controlling the number of vertical
#' grid lines, see panel.grid for details.
#' @param \dots additional display parameters are allowed. Those typically
#' take the value of a valid R colour descriptors. The parameter names will
#' later be matched to optional track item types as defined in the 'feature'
#' range attribute, and all tracks of the matched types are coloured
#' accordingly. See the documentation of the `GeneRegionTrack` and
#' `AnnotationTrack` classes as well as grouping for details.