@@ -1,6 +1,6 @@

 Package: Gviz

 Title: Plotting data and annotation information along genomic coordinates

-Version: 1.42.0

+Version: 1.42.1

 Authors@R: c(person("Florian", "Hahne", role="aut"),

 	 person("Steffen", "Durinck", role="aut"),

 	 person("Robert", "Ivanek", role=c("aut", "cre"), 

@@ -23,7 +23,7 @@ Description: Genomic data analyses requires integrated visualization

     your data.

 LazyLoad: yes

 Encoding: UTF-8

-RoxygenNote: 7.1.2

+RoxygenNote: 7.2.3.9001 

 Roxygen: list(markdown = TRUE)

 Depends:

     R (>= 4.2),

@@ -1,5 +1,6 @@

 # Generated by roxygen2: do not edit by hand

+export(.DisplayPars)

 export(.chrName)

 export(.doCache)

 export(AlignmentsTrack)

@@ -27,12 +27,12 @@ setClassUnion("SequenceTrackOrNULL", c("SequenceTrack", "NULL"))

 #'

 #' \describe{

 #'

-#' \item{}{A \code{character} string: the path to a \code{BAM} file containing

+#' \item{A \code{character} string:}{ the path to a \code{BAM} file containing

 #' the read alignments. To be precise, this will result in the instantiation of

 #' a \code{ReferenceAlignmentsTrack} object, but for the user this

 #' implementation detail should be of no concern.}

 #'

-#' \item{}{A \code{GRanges} object: the genomic ranges of the individual reads

+#' \item{A \code{GRanges} object:}{ the genomic ranges of the individual reads

 #' as well as the optional additional metadata columns \code{id}, \code{cigar},

 #' \code{mapq}, \code{flag}, \code{isize}, \code{groupid}, \code{status},

 #' \code{md} and \code{seqs} (see description of the individual function

@@ -40,7 +40,7 @@ setClassUnion("SequenceTrackOrNULL", c("SequenceTrack", "NULL"))

 #' object without further arguments, e.g. \code{AlignmentsTrack(range=obj)} is

 #' equivalent to calling the coerce method \code{as(obj, "AlignmentsTrack")}.}

 #'

-#' \item{}{An \code{\linkS4class{IRanges}} object: almost identical to the

+#' \item{An \code{\linkS4class{IRanges}} object:}{ almost identical to the

 #' \code{GRanges} case, except that the chromosome and strand information as

 #' well as all additional metadata has to be provided in the separate

 #' \code{chromosome}, \code{strand}, \code{feature}, \code{group} or \code{id}

@@ -49,7 +49,7 @@ setClassUnion("SequenceTrackOrNULL", c("SequenceTrack", "NULL"))

 #' explicitely the more or less reasonable default values \code{chromosome=NA}

 #' and \code{strand="*"} are used. }

 #'

-#' \item{}{A \code{data.frame} object: the \code{data.frame} needs to contain

+#' \item{A \code{data.frame} object:}{ the \code{data.frame} needs to contain

 #' at least the two mandatory columns \code{start} and \code{end} with the

 #' range coordinates. It may also contain a \code{chromosome} and a

 #' \code{strand} column with the chromosome and strand information for each

@@ -17,64 +17,64 @@ NULL

 #'

 #' \describe{

 #'

-#' \item{}{\code{p}: simple xy-plot.}

+#' \item{\code{p}:}{ simple xy-plot.}

 #'

-#' \item{}{\code{l}: lines plot. In the case of multiple samples this plotting

+#' \item{\code{l}:}{ lines plot. In the case of multiple samples this plotting

 #' type is not overly usefull since the points in the data matrix are connected

 #' in column-wise order. Type \code{a} might be more appropriate in these

 #' situations.}

 #'

-#' \item{}{\code{b}: combination of xy-plot and lines plot.}

+#' \item{\code{b}:}{ combination of xy-plot and lines plot.}

 #'

-#' \item{}{\code{a}: lines plot of the column-wise average values.}

+#' \item{\code{a}:}{ lines plot of the column-wise average values.}

 #'

-#' \item{}{\code{s}: sort and connect data points along the x-axis}

+#' \item{\code{s}:}{ sort and connect data points along the x-axis}

 #'

-#' \item{}{\code{S}: sort and connect data points along the y-axis}

+#' \item{\code{S}:}{ sort and connect data points along the y-axis}

 #'

-#' \item{}{\code{g}: add grid lines. To ensure a consitant look and feel across

+#' \item{\code{g}:}{ add grid lines. To ensure a consitant look and feel across

 #' multiple tracks, grid lines should preferentially be added by using the

 #' \code{grid} display parameter.}

 #'

-#' \item{}{\code{r}: add a regression line to the plot.}

+#' \item{\code{r}:}{ add a regression line to the plot.}

 #'

-#' \item{}{\code{h}: histogram-like vertical lines centered in the middle of

+#' \item{\code{h}:}{ histogram-like vertical lines centered in the middle of

 #' the coordinate ranges.}

 #'

-#' \item{}{\code{smooth}: add a loess fit to the plot. The following display

+#' \item{\code{smooth}:}{ add a loess fit to the plot. The following display

 #' parameters can be used to control the loess calculation: \code{span, degree,

 #' family, evaluation}. See \code{\link{panel.loess}} for details.}

 #'

-#' \item{}{\code{histogram}: plot data as a histogram, where the width of the

+#' \item{\code{histogram}:}{ plot data as a histogram, where the width of the

 #' histogram bars reflects the width of the genomic ranges in the \code{range}

 #' slot.}

 #'

-#' \item{}{\code{mountain}: plot a smoothed version of the data relative to a

+#' \item{\code{mountain}:}{ plot a smoothed version of the data relative to a

 #' baseline, as defined by the \code{baseline} display parameter. The following

 #' display parameters can be used to control the smoothing: \code{span, degree,

 #' family, evaluation}. See \code{\link{panel.loess}} for details. The layout

 #' of the plot can be further customized via the following display parameters:

 #' \code{col.mountain, lwd.mountain, lty.mountain, fill.mountain}.}

 #'

-#' \item{}{\code{polygon}: plot data as a polygon (similar to

+#' \item{\code{polygon}:}{ plot data as a polygon (similar to

 #' \code{mountain}-type but without smoothing). Data are plotted relative to a

 #' baseline, as defined by the \code{baseline} display parameter. The layout of

 #' the plot can be further customized via the following display parameters:

 #' \code{col.mountain, lwd.mountain, lty.mountain, fill.mountain}.}

 #'

-#' \item{}{\code{boxplot}: plot the data as box-and-whisker plots. The layout

+#' \item{\code{boxplot}:}{ plot the data as box-and-whisker plots. The layout

 #' of the plot can be further customized via the following display parameters:

 #' \code{box.ratio, box.width, varwidt, notch, notch.frac, levels.fos, stats,

 #' coef, do.out}. See \code{\link{panel.bwplot}} for details.}

 #'

-#' \item{}{\code{gradient}: collapse the data across samples and plot this

+#' \item{\code{gradient}:}{ collapse the data across samples and plot this

 #' average value as a color-coded gradient. Essenitally this is similar to the

 #' heatmap-type plot of a single sample. The layout of the plot can be further

 #' customized via the display parameters \code{ncolor} and \code{gradient}

 #' which control the number of gradient colors as well as the gradient base

 #' colors, respectively.}

 #'

-#' \item{}{\code{heatmap}: plot the color-coded values for all samples in the

+#' \item{\code{heatmap}:}{ plot the color-coded values for all samples in the

 #' form of a heatmap. The data for individual samples can be visually separated

 #' by setting the \code{separator} display parameter. It's value is taken as

 #' the amount of spacing in pixels in between two heatmap rows. The layout of

@@ -82,7 +82,7 @@ NULL

 #' and \code{gradient} which control the number of gradient colors as well as

 #' the gradient base colors, respectively.}

 #'

-#' \item{}{\code{horizon}: plot continuous data by cutting the y range into

+#' \item{\code{horizon}:}{ plot continuous data by cutting the y range into

 #' segments and overplotting them with color representing the magnitude and

 #' direction of deviation. This is particularly useful when comparing multiple

 #' samples, in which case the horizon strips are stacked. See

@@ -937,7 +937,7 @@ setMethod("drawGD", signature("DataTrack"), function(GdObject, minBase, maxBase,

     vals <- values(GdObject)

     groups <- .dpOrDefault(GdObject, "groups")

     if (!is.null(groups) && length(groups) != nrow(vals)) {

-        stop("'groups' must be a vector of similar length as the number of rows in the data matrix (", nrow(vals), ")")

+        stop("'groups' must be a vector of the same length as the number of rows in the data matrix (", nrow(vals), ")")

     }

     if (!is.null(groups) && !is.factor(groups)) {

         groups <- factor(groups)

@@ -59,7 +59,7 @@ NULL

 #'

 #' \describe{

 #'

-#' \item{}{A \code{TxDb} object: all the necessary gene model information

+#' \item{A \code{TxDb} object:}{ all the necessary gene model information

 #' including exon locations, transcript groupings and associated gene ids are

 #' contained in \code{TxDb} objects, and the coercion between the two is almost

 #' completely automated. If desired, the data to be fetched from the

@@ -70,7 +70,7 @@ NULL

 #' coding region information that is part of the original \code{TxDb} object is

 #' retained in the \code{GeneRegionTrack}.}

 #'

-#' \item{}{A \code{GRanges} object: the genomic ranges for the

+#' \item{A \code{GRanges} object:}{ the genomic ranges for the

 #' \code{GeneRegion} track as well as the optional additional metadata columns

 #' \code{feature}, \code{transcript}, \code{gene}, \code{exon} and

 #' \code{symbol} (see description of the individual function parameters below

@@ -78,7 +78,7 @@ NULL

 #' further arguments, e.g.  \code{GeneRegionTrack(range=obj)} is equivalent to

 #' calling the coerce method \code{as(obj, "GeneRegionTrack")}.}

 #'

-#' \item{}{A \code{GRangesList} object: this is very similar to the previous

+#' \item{A \code{GRangesList} object:}{ this is very similar to the previous

 #' case, except that the grouping information that is part of the list

 #' structure is preserved in the \code{GeneRegionTrack}. I.e., all the elements

 #' within one list item receive the same group id. For consistancy, there is

@@ -88,7 +88,7 @@ NULL

 #' data slots, the object will not be particularly useful, because all the

 #' identifiers will be set to a common default value.}

 #'

-#' \item{}{An \code{\linkS4class{IRanges}} object: almost identical to the

+#' \item{An \code{\linkS4class{IRanges}} object:}{ almost identical to the

 #' \code{GRanges} case, except that the chromosome and strand information as

 #' well as all additional data has to be provided in the separate

 #' \code{chromosome}, \code{strand}, \code{feature}, \code{transcript},

@@ -99,7 +99,7 @@ NULL

 #' providing information about the gene-to-transcript relationship or the

 #' human-readble symbols renders a lot of the class' functionality useles.}

 #'

-#' \item{}{A \code{data.frame} object: the \code{data.frame} needs to contain

+#' \item{A \code{data.frame} object:}{ the \code{data.frame} needs to contain

 #' at least the two mandatory columns \code{start} and \code{end} with the

 #' range coordinates. It may also contain a \code{chromosome} and a

 #' \code{strand} column with the chromosome and strand information for each

@@ -109,7 +109,7 @@ NULL

 #' \code{symbol} data can be provided as columns in the \code{data.frame}. The

 #' above comments about potential default values also apply here.}

 #'

-#' \item{}{A \code{character} scalar: in this case the value of the

+#' \item{A \code{character} scalar:}{ in this case the value of the

 #' \code{range} argument is considered to be a file path to an annotation file

 #' on disk. A range of file types are supported by the \code{Gviz} package as

 #' identified by the file extension. See the \code{importFunction}

@@ -23,16 +23,16 @@ NULL

 #'

 #' \describe{

 #'

-#' \item{}{An object of class \code{\linkS4class{DNAStringSet}}. The individual

+#' \item{An object of class \code{\linkS4class{DNAStringSet}}.}{ The individual

 #' \code{\linkS4class{DNAString}}s are considered to be the different

 #' chromosome sequences.}

 #'

-#' \item{}{An object of class \code{\linkS4class{BSgenome}}. The \code{Gviz}

+#' \item{An object of class \code{\linkS4class{BSgenome}}.}{ The \code{Gviz}

 #' package tries to follow the \code{BSgenome} philosophy in that the

 #' respective chromosome sequences are only realized once they are first

 #' accessed.}

 #'

-#' \item{}{A \code{character} scalar: in this case the value of the

+#' \item{A \code{character} scalar:}{ in this case the value of the

 #' \code{sequence} argument is considered to be a file path to an annotation

 #' file on disk. A range of file types are supported by the \code{Gviz} package

 #' as identified by the file extension. See the \code{importFunction}

@@ -315,7 +315,7 @@ UcscTrack <- function(track, table = NULL,

     }

     args <- lapply(list(...), function(x) {

         if (is.character(x) && length(x) == 1) {

-            if (!x %in% colnames(tableDat)) x else tableDat[, x]

+            if (!x %in% colnames(tableDat)) x else unlist(tableDat[, x])

         } else {

             x

         }

@@ -89,83 +89,83 @@

 #'

 #' \describe{

 #'

-#' \item{GenomeAxisTrack}{:

+#' \item{GenomeAxisTrack:}{

 #'

 #' \describe{

 #'

-#' \item{}{\code{add35=FALSE}: Logical scalar. Add 3' to 5' direction

+#' \item{\code{add35=FALSE}:}{ Logical scalar. Add 3' to 5' direction

 #' indicators.}

 #'

-#' \item{}{\code{add53=FALSE}: Logical scalar. Add 5' to 3' direction

+#' \item{\code{add53=FALSE}:}{ Logical scalar. Add 5' to 3' direction

 #' indicators.}

 #'

-#' \item{}{\code{background.title="transparent"}: Character scalar.  The

+#' \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

+#' \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

+#' \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.

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \item{\code{fontsize=10}:}{ Numeric scalar. Font size for the axis

 #' annotation text in points.}

 #'

-#' \item{}{\code{labelPos="alternating"}: Character vector, one in

+#' \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

+#' \item{\code{littleTicks=FALSE}:}{ Logical scalar. Add more fine-grained tick

 #' marks.}

 #'

-#' \item{}{\code{lwd=2}: Numeric scalar. The line width for the axis

+#' \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

+#' \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

+#' \item{\code{showId=FALSE}:}{ Logical scalar. Show the optional range

 #' highlighting annotation.}

 #'

-#' \item{}{\code{showTitle=FALSE}: Logical scalar. Plot a title panel. Defaults

+#' \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

+#' \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.

+#' \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

+#' \item{\code{col="darkgray"}:}{ Character scalar. The color for the axis

 #' lines and tickmarks.}

 #'

 #' }

@@ -174,135 +174,135 @@

 #'

 #' \describe{

 #'

-#' \item{}{\code{alpha=1}: Numeric scalar. The transparency for all track

+#' \item{\code{alpha=1}:}{ Numeric scalar. The transparency for all track

 #' items.}

 #'

-#' \item{}{\code{alpha.title=NULL}: Numeric scalar. The transparency for the

+#' \item{\code{alpha.title=NULL}:}{ Numeric scalar. The transparency for the

 #' title panel.}

 #'

-#' \item{}{\code{background.panel="transparent"}: Integer or character scalar.

+#' \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.

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \item{\code{grid=FALSE}:}{ Boolean, switching on/off the plotting of a

 #' grid.}

 #'

-#' \item{}{\code{h=-1}: Integer scalar. Parameter controlling the number of

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \item{\code{v=-1}:}{ Integer scalar. Parameter controlling the number of

 #' vertical grid lines, see \code{\link{panel.grid}} for details.}

 #'

 #' }

 #'

 #' }

 #'

-#' \item{DataTrack}{:

+#' \item{DataTrack:}{

 #'

 #' \describe{

 #'

-#' \item{}{\code{aggregateGroups=FALSE}: Logical scalar. Aggregate the values

+#' \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

+#' \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

@@ -310,223 +310,223 @@

 #' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \item{\code{box.legend=FALSE}:}{ Logical scalar. Draw a box around a

 #' legend.}

 #'

-#' \item{}{\code{box.ratio=1}: Numeric scalar. Parameter controlling the

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \item{\code{collapse=FALSE}:}{ Logical scalar. Collapse overlapping ranges

 #' and aggregate the underlying data.}

 #'

-#' \item{}{\code{degree=1}: Numeric scalar. Parameter controlling the loess

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \item{\code{fontsize.legend=NULL}:}{ Numeric scalar. The pixel size for the

 #' legend text.}

 #'

-#' \item{}{\code{fontcolor.legend="#808080"}: Integer or character scalar. The

+#' \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.

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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.

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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

+#' \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},

@@ -534,10 +534,10 @@

 #' \code{\linkS4class{DataTrack}} for more information on the individual

 #' plotting types.}

 #'

-#' \item{}{\code{varwidth=FALSE}: Logical scalar. Parameter controlling the

+#' \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

+#' \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.

@@ -545,13 +545,13 @@

 #' 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

+#' \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

+#' \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

+#' \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.}

 #'

@@ -561,204 +561,204 @@

 #'

 #' \describe{

 #'

-#' \item{}{\code{alpha=1}: Numeric scalar. The transparency for all track

+#' \item{\code{alpha=1}:}{ Numeric scalar. The transparency for all track

 #' items.}

 #'

-#' \item{}{\code{alpha.title=NULL}: Numeric scalar. The transparency for the

+#' \item{\code{alpha.title=NULL}:}{ Numeric scalar. The transparency for the

 #' title panel.}

 #'

-#' \item{}{\code{background.panel="transparent"}: Integer or character scalar.

+#' \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.

+#' \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.

+#' \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

+#' \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

+#' \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