@@ -6,10 +6,11 @@

 ^\.Rproj\.user$

 ^\.Rbuildignore$

 ^\.gitignore$

+^\.git$

 ^\.github$

 ^\.travis\.yml$

 ^\.codecov\.yml$

 ^Dockerfile$

 ^LICENSE$

 ^Rplots\.pdf$

-^vignettes\/Gviz-logo\.pdf$

\ No newline at end of file

+^vignettes\/Gviz-logo\.pdf$

@@ -660,16 +660,14 @@ setMethod("initialize", "AnnotationTrack", function(.Object, ...) {

     if (is.null(list(...)$range) && is.null(list(...)$genome) && is.null(list(...)$chromosome)) {

         return(.Object)

     }

-    ## the diplay parameter defaults

+    ## the display parameter defaults

     .makeParMapping()

     .Object <- .updatePars(.Object, "AnnotationTrack")

     range <- list(...)$range

     if (!is.null(range) && length(.Object)) {

         if (!all(.Object@columns %in% colnames(values(range)))) {

-            stop(paste(

-                "Problem initializing AnnotationTrack need the following columns:",

-                paste(.Object@columns, collpase = ", ")

-            ), "\n")

+            stop("Problem initializing AnnotationTrack, need the following columns:",

+                toString(.Object@columns, collapse = ", "))

         }

         grp <- if (is(.Object, "GeneRegionTrack")) values(range)$transcript else values(range)$group

         if (any(vapply(split(as.character(strand(range)), grp), function(x) length(unique(x)), numeric(1)) != 1)) {

@@ -35,7 +35,7 @@ setMethod("seqnames", "SequenceBSgenomeTrack", function(x) as.character(seqnames

 setMethod("seqlevels", "RangeTrack", function(x) unique(seqnames(x)))

 setMethod("seqlevels", "SequenceDNAStringSetTrack", function(x) seqnames(x)[width(x@sequence) > 0])

 setMethod("seqlevels", "SequenceRNAStringSetTrack", function(x) seqnames(x)[width(x@sequence) > 0])

-setMethod("seqlevels", "SequenceBSgenomeTrack", function(x) seqnames(x)[bsapply(new("BSParams", X = x@sequence, FUN = length, simplify = T)) > 0]) # maybe seqnames only to speed-up

+setMethod("seqlevels", "SequenceBSgenomeTrack", function(x) seqnames(x)[bsapply(new("BSParams", X = x@sequence, FUN = length, simplify = TRUE)) > 0]) # maybe seqnames only, to speed-up

 setMethod("seqinfo", "RangeTrack", function(x) table(seqnames(x)))

 ## Min and max ranges

@@ -205,7 +205,7 @@ setMethod("subseq", "ReferenceSequenceTrack", function(x, start = NA, end = NA,

     if (!is.na(start[1] + end[1] + width[1])) {

         warning("All 'start', 'stop' and 'width' are provided, ignoring 'width'")

         width <- NA

-    } 

+    }

     ## We want start and end to be set if width is provided

     if (!is.na(width[1])) {

         if (is.na(start) && is.na(end)) {

@@ -1015,9 +1015,9 @@ setMethod(

         switch(agFun,

                "mean" = runmean,

                "sum" = runsum,

-               "median" = runmed2 <-  function(x, k, na.rm=FALSE, ...) { 

+               "median" = runmed2 <-  function(x, k, na.rm=FALSE, ...) {

                    na.action <- if (na.rm) { "na.omit" } else { "+Big_alternate" }

-                       runmed(x=as.numeric(x), k=k, na.action=na.action) 

+                       runmed(x=as.numeric(x), k=k, na.action=na.action)

                    },

                "min" = runqmin <- function(x, k, i=1, ...) { runq(x=x, k=k, i=i, ...) },

                "max" = runqmax <- function(x, k, i=k, ...) { runq(x=x, k=k, i=i, ...) },

@@ -1026,7 +1026,7 @@ setMethod(

     } else {

         if (is.function(agFun)) {

             function(x, k, na.rm=FALSE, endrule="constant") {

-                ans <- vapply(0:(length(x)-k), function(offset) agFun(x[1:k + offset], na.rm=na.rm), FUN.VALUE = numeric(1))

+                ans <- vapply(0:(length(x)-k), function(offset) agFun(x[seq_len(k) + offset], na.rm=na.rm), FUN.VALUE = numeric(1))

                 ans <- Rle(ans)

                 if (endrule == "constant") {

                     j <- (k + 1L)%/%2L

@@ -2752,11 +2752,7 @@ setMethod("drawGD", signature("GenomeAxisTrack"), function(GdObject, minBase, ma

     if (!is.null(scaleLen)) {

         len <- (maxBase - minBase + 1)

         if (scaleLen > len) {

-            warning(paste("scale (", scaleLen,

-                ") cannot be larger than plotted region",

-                len, " - setting to ~5%\n",

-                sep = ""

-            ))

+            warning(sprintf("scale (%d) cannot be larger than plotted region %d - setting to ~5%\n", scaleLen, len))

             scaleLen <- 0.05

         }

         xoff <- len * 0.03 + minBase

@@ -3624,21 +3620,21 @@ setMethod("drawGD", signature("DataTrack"), function(GdObject, minBase, maxBase,

             na_idx <- which(is.na(upper))

             ## case 1. there are no error bars to plot at all

             if (length(na_idx) == length(upper)) {

-                if (debugMode) cat("\t Case 1: all empty. returning\n")

+                if (debugMode) message("\t Case 1: all empty. returning")

                 return(TRUE)

                 ## case 2. no missing points

             } else if (length(na_idx) < 1) {

-                if (debugMode) cat("\t Case 2: one continuous polygon\n")

+                if (debugMode) message("\t Case 2: one continuous polygon")

                 panel.polygon(c(x, rev(x)), c(upper, rev(lower)),

                     border = col, col = fill, alpha = alpha, ...

                 )

                 ## case 3. have complete data with some or no missing points

             } else {

                 curr_start <- min(which(!is.na(upper)))

-                if (debugMode) cat(sprintf("\t Case 3: %i of %i NA\n", length(na_idx), length(upper)))

+                if (debugMode) message(sprintf("\t Case 3: %i of %i NA", length(na_idx), length(upper)))

                 curr_na_pos <- 1

                 while (curr_na_pos <= length(na_idx)) {

-                    if (debugMode) cat(sprintf("\t\tcurr_na_pos = %i, na_idx length= %i\n", curr_na_pos, length(na_idx)))

+                    if (debugMode) message(sprintf("\t\tcurr_na_pos = %i, na_idx length= %i", curr_na_pos, length(na_idx)))

                     ## complete the current poly

                     idx <- curr_start:(na_idx[curr_na_pos] - 1)

                     panel.polygon(c(x[idx], rev(x[idx])), c(upper[idx], rev(lower[idx])),

@@ -3646,7 +3642,7 @@ setMethod("drawGD", signature("DataTrack"), function(GdObject, minBase, maxBase,

                     )

                     ## contiguous empty spots - skip

                     while ((na_idx[curr_na_pos + 1] == na_idx[curr_na_pos] + 1) && (curr_na_pos < length(na_idx))) {

-                        if (debugMode) cat(sprintf("\t\ttight-loop:curr_na_pos = %i\n", curr_na_pos))

+                        if (debugMode) message(sprintf("\t\ttight-loop:curr_na_pos = %i", curr_na_pos))

                         curr_na_pos <- curr_na_pos + 1

                     }

                     ## at this point, either we've finished NA spots or the next one is far away.

@@ -3656,7 +3652,7 @@ setMethod("drawGD", signature("DataTrack"), function(GdObject, minBase, maxBase,

                 }

                 ## there is one last polygon at the end of the view range

                 if (na_idx[length(na_idx)] < length(upper)) {

-                    if (debugMode) cat("\tWrapping last polygon\n")

+                    if (debugMode) message("\tWrapping last polygon")

                     idx <- curr_start:length(upper)

                     panel.polygon(c(x[idx], rev(x[idx])), c(upper[idx], rev(lower[idx])),

                         col = fill, border = col, alpha = alpha, ...

@@ -3699,7 +3695,7 @@ setMethod("drawGD", signature("DataTrack"), function(GdObject, minBase, maxBase,

             names(fill) <- NULL

             for (j in seq_along(by)) {

                 g <- names(by)[j]

-                if (debugMode) print(g)

+                if (debugMode) message(g)

                 df <- data.frame(

                     x = position(GdObject), y = mu[[j]],

                     low = mu[[j]] - confint[[j]], high = mu[[j]] + confint[[j]],

@@ -4781,8 +4777,8 @@ setMethod("show", signature(object = "OverlayTrack"), function(object) {

 ## A helper function to plot general information about a ReferenceTrack

 .referenceTrackInfo <- function(object, type) {

-    cat(sprintf(

-        "%s '%s'\n| genome: %s\n| active chromosome: %s\n| referenced file: %s\n",

+    message(sprintf(

+        "%s '%s'\n| genome: %s\n| active chromosome: %s\n| referenced file: %s",

         type,

         names(object),

         genome(object),

@@ -4790,7 +4786,7 @@ setMethod("show", signature(object = "OverlayTrack"), function(object) {

         object@reference

     ))

     if (length(object@mapping) && type != "ReferenceDataTrack") {

-          cat(sprintf("| mapping: %s\n", paste(names(object@mapping), as.character(object@mapping), sep = "=", collapse = ", ")))

+          message(sprintf("| mapping: %s\n", paste(names(object@mapping), as.character(object@mapping), sep = "=", collapse = ", ")))

       }

 }

@@ -55,11 +55,11 @@

 ## We want to deal with chromosomes in a reasonable way. This coerces likely inputs to a unified

 ## chromosome name as understood by UCSC. Accepted inputs are:

-##    - a single integer or a character coercable to one or integer-character combinations

+##    - a single integer or a character coercible to one or integer-character combinations

 ##    - a character, starting with 'chr' (case insensitive)

 ## Arguments:

 ##    o x: a character string to be converted to a valid UCSC chromosome name

-##    o force: a logical flag, force prepending of 'chr' if missing

+##    o force: a logical flag, force pre-pending of 'chr' if missing

 ## Value: the UCSC character name

 .chrName <- function(x, force = FALSE) {

     if (!getOption("ucscChromosomeNames") || length(x) == 0) {

@@ -86,10 +86,9 @@

             head <- TRUE

         }

         if (!head) {

-            stop(sprintf(paste(

-                "Invalid chromosome identifier '%s'\nPlease consider setting options(ucscChromosomeNames=FALSE)",

-                "to allow for arbitrary chromosome identifiers."

-            ), y))

+            stop(sprintf("Invalid chromosome identifier '%s'\n", y),

+                 "Please consider setting options(ucscChromosomeNames=FALSE) ",

+                 "to allow for arbitrary chromosome identifiers.")

         }

         substring(y, 1, 3) <- tolower(substring(y, 1, 3))

         y

@@ -113,7 +112,7 @@

 ## unimplemented types...

 ## Arguments:

 ##    o GdObject: an object inheriting from class GdObject

-## Value: a logical skalar indicating whether stacking is needed or not

+## Value: a logical scalar indicating whether stacking is needed or not

 .needsStacking <- function(GdObject) stacking(GdObject) %in% c("squish", "pack", "full")

@@ -1434,38 +1433,25 @@ addScheme <- function(scheme, name) {

         ds <- listDatasets(bm)

         mt <- ds[match(map$dataset, ds$dataset), "version"]

         if (is.na(mt)) {

-            stop(sprintf(paste(

-                "Gviz thinks that the UCSC genome identifier '%s' should map to the Biomart data set '%s' which is not correct.",

-                "\nPlease manually provide biomaRt object"

-            ), genome, map$dataset))

+            stop(sprintf("Gviz thinks that the UCSC genome identifier '%s' should map to the Biomart data set '%s' which is not correct.",

+                         genome, map$dataset), "\nPlease manually provide biomaRt object")

         }

         if (mt != map$value) {

-            stop(sprintf(

-                paste(

-                    "Gviz thinks that the UCSC genome identifier '%s' should map to the current Biomart head as '%s',",

-                    "but its current version is '%s'.\nPlease manually provide biomaRt object"

-                ),

-                genome, map$value, mt

-            ))

+            stop(sprintf("Gviz thinks that the UCSC genome identifier '%s' should map to the current Biomart head as '%s', ",

+                         genome, map$value, mt), "but its current version is '%s'.\nPlease manually provide biomaRt object.")

         }

     } else {

         bm <- useEnsembl(biomart = "ENSEMBL_MART_ENSEMBL", dataset = map$dataset, host = sprintf("%s.archive.ensembl.org", tolower(sub(".", "", map$date, fixed = TRUE))))

         ds <- listDatasets(bm)

         mt <- ds[match(map$dataset, ds$dataset), "version"]

         if (is.na(mt)) {

-            stop(sprintf(paste(

-                "Gviz thinks that the UCSC genome identifier '%s' should map to the Biomart data set '%s' which is not correct.",

-                "\nPlease manually provide biomaRt object"

-            ), genome, map$dataset))

+            stop(sprintf("Gviz thinks that the UCSC genome identifier '%s' should map to the Biomart data set '%s' which is not correct.",

+                         genome, map$dataset), "\nPlease manually provide biomaRt object")

         }

         if (mt != map$value) {

-            stop(sprintf(

-                paste(

-                    "Gviz thinks that the UCSC genome identifier '%s' should map to Biomart archive %s (version %s) as '%s',",

-                    "but its version is '%s'.\nPlease manually provide biomaRt object"

-                ),

-                genome, sub(".", " ", map$date, fixed = TRUE), map$version, map$value, mt

-            ))

+            stop(sprintf("Gviz thinks that the UCSC genome identifier '%s' should map to Biomart archive %s (version %s) as '%s',",

+                         genome, sub(".", " ", map$date, fixed = TRUE), map$version, map$value, mt),

+                 "but its version is '%s'.\nPlease manually provide biomaRt object")

         }

     }

     return(bm)

@@ -2216,7 +2202,7 @@ availableDisplayPars <- function(class) {

       }

     class <- match.arg(class, c(

         "GdObject", "GenomeAxisTrack", "RangeTrack", "NumericTrack", "DataTrack", "IdeogramTrack", "StackedTrack",

-        "AnnotationTrack", "DetailsAnnotationTrack", "GeneRegionTrack", "BiomartGeneRegionTrack", 

+        "AnnotationTrack", "DetailsAnnotationTrack", "GeneRegionTrack", "BiomartGeneRegionTrack",

         "AlignmentsTrack", "SequenceTrack", "SequenceBSgenomeTrack", "SequenceDNAStringSetTrack", "SequenceRNAStringSetTrack"

     ))

     parents <- names(getClassDef(class)@contains)

@@ -2372,10 +2358,8 @@ availableDisplayPars <- function(class) {

         dat

     })

     if (is(res, "try-error")) {

-        warning(sprintf(paste(

-            "File '%s' is not valid according to the GFF3 standard and can not be properly parsed.",

-            "Results may not be what you expected!"

-        ), file))

+        warning(sprintf("File '%s' is not valid according to the GFF3 standard and can not be properly parsed.",

+                        file), "\nResults may not be what you expected!")

         res <- dat

     }

     return(res)

@@ -2804,13 +2788,8 @@ availableDefaultMapping <- function(file, trackType) {

         vm[[inputType]] <- setNames(list(list(".stream" = stream)), trackType)

     } else {

         if (is.null(vm[[inputType]]) || is.null(vm[[inputType]][[trackType]])) {

-            warning(sprintf(

-                paste(

-                    "There are no default mappings from %s files to %s. Please provide a manual mapping",

-                    "in the track constructor if you haven't already done so."

-                ),

-                inputType, trackType

-            ))

+            warning(sprintf("There are no default mappings from %s files to %s. Please provide a manual mapping",

+                            inputType, trackType), " in the track constructor if you haven't already done so.")

             vm[[inputType]] <- setNames(list(list(".stream" = stream)), trackType)

         }

     }

@@ -821,7 +821,7 @@ updateDocumentation <- function(outdir="~/Rpacks/Gviz/man")

 ## run

 ##       compareDtContent(<className>, <documentationDir>, details)

 ## and check the results. This should show you what is different between the current man page file and the central definitions

-## It will also find things that may have been added/edited manually in the man page file, and might need backporting into the

+## It will also find things that may have been added/edited manually in the man page file, and might need back-porting into the

 ## central definition list.

 ## When you are happy with the results, run

 ##       updateRdFile(<className>, <documentationDir>)

@@ -2357,223 +2357,6 @@ getScheme(name=getOption("Gviz.scheme"))

     } 

-    \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", "polygon", "h", "boxplot", "gradient",

-          "heatmap", "horizon")}. See the 'Details' section in

-          \code{\linkS4class{DataTrack}} for more information on the

-          individual plotting types.} 

-

-        \item{}{\code{fill="#0080ff"}: the fill color for the coverage

-          indicator.} 

-

-        \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.} 

-

-      } 

-

-      \bold{\emph{Inherited from class StackedTrack:}} 

-

-      \describe{ 

-

-        \item{}{\code{stackHeight=0.75}: Numeric between 0 and 1.

-          Controls the vertical size and spacing between stacked

-          elements. The number defines the proportion of the total

-          available space for the stack that is used to draw the glyphs.

-          E.g., a value of 0.5 means that half of the available vertical

-          drawing space (for each stacking line) is used for the glyphs,

-          and thus one quarter of the available space each is used for

-          spacing above and below the glyph. Defaults to 0.75.} 

-

-        \item{}{\code{reverseStacking=FALSE}: Logical flag. Reverse

-          the y-ordering of stacked items. I.e., features that are

-          plotted on the bottom-most stacks will be moved to the top-most

-          stack and vice versa.} 

-

-      } 

-

-      \bold{\emph{Inherited from class GdObject:}} 

-

-      \describe{ 

-

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

-          all track items.} 

-

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

-          for the title panel.} 

-

-        \item{}{\code{background.panel="transparent"}: Integer or

-          character scalar. The background color of the content panel.} 

-

-        \item{}{\code{background.title="lightgray"}: Integer or character

-          scalar. The background color for the title panel.} 

-

-        \item{}{\code{background.legend="transparent"}: Integer or

-          character scalar. The background color for the legend.} 

-

-        \item{}{\code{cex.axis=NULL}: Numeric scalar. The expansion

-          factor for the axis annotation. Defaults to \code{NULL}, in

-          which case it is automatically determined based on the

-          available space.} 

-

-        \item{}{\code{cex.title=NULL}: Numeric scalar. The expansion

-          factor for the title panel. This effects the fontsize of both

-          the title and the axis, if any. Defaults to \code{NULL},

-          which means that the text size is automatically adjusted to

-          the available space.} 

-

-        \item{}{\code{cex=1}: Numeric scalar. The overall font expansion

-          factor for all text and glyphs, unless a more specific

-          definition exists.} 

-

-        \item{}{\code{col.axis="white"}: Integer or character scalar.

-          The font and line color for the y axis, if any.} 

-

-        \item{}{\code{col.border.title="white"}: Integer or character

-          scalar. The border color for the title panels.} 

-

-        \item{}{\code{col.frame="lightgray"}: Integer or character

-          scalar. The line color used for the panel frame, if

-          \code{frame==TRUE}} 

-

-        \item{}{\code{col.grid="#808080"}: Integer or character scalar.

-          Default line color for grid lines, both when \code{type=="g"}

-          in \code{\link{DataTrack}}s and when display parameter

-          \code{grid==TRUE}.} 

-

-        \item{}{\code{col.line=NULL}: Integer or character scalar.

-          Default colors for plot lines. Usually the same as the global

-          \code{col} parameter.} 

-

-        \item{}{\code{col.symbol=NULL}: Integer or character scalar.

-          Default colors for plot symbols. Usually the same as the

-          global \code{col} parameter.} 

-

-        \item{}{\code{col.title="white"}: Integer or character scalar.

-          The border color for the title panels} 

-

-        \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{fontcolor="black"}: Integer or character scalar.

-          The font color for all text, unless a more specific definition

-          exists.} 

-

-        \item{}{\code{fontface.title=2}: Integer or character scalar.

-          The font face for the title panels.} 

-

-        \item{}{\code{fontface=1}: Integer or character scalar. The

-          font face for all text, unless a more specific definition exists.} 

-

-        \item{}{\code{fontfamily.title="sans"}: Integer or character

-          scalar. The font family for the title panels.} 

-

-        \item{}{\code{fontfamily="sans"}: Integer or character scalar.

-          The font family for all text, unless a more specific definition

-          exists.} 

-

-        \item{}{\code{fontsize=12}: Numeric scalar. The font size for

-          all text, unless a more specific definition exists.} 

-

-        \item{}{\code{frame=FALSE}: Boolean. Draw a frame around the

-          track when plotting.} 

-

-        \item{}{\code{grid=FALSE}: Boolean, switching on/off the plotting

-          of a grid.} 

-

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

-          number of horizontal grid lines, see \code{\link{panel.grid}}

-          for details.} 

-

-        \item{}{\code{lineheight=1}: Numeric scalar. The font line

-          height for all text, unless a more specific definition exists.} 

-

-        \item{}{\code{lty.grid="solid"}: Integer or character scalar.

-          Default line type for grid lines, both when \code{type=="g"}

-          in \code{\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{lwd.border.title=1}: Integer scalar. The border

-          width for the title panels.} 

-

-        \item{}{\code{lwd.title=1}: Integer scalar. The border width

-          for the title panels} 

-

-        \item{}{\code{lwd.grid=1}: Numeric scalar. Default line width

-          for grid lines, both when \code{type=="g"} in \code{\link{DataTrack}}s

-          and when display parameter \code{grid==TRUE}.} 

-

-        \item{}{\code{lwd=1}: Numeric scalar. Default line width setting

-          for all plotting elements, unless there is a more specific

-          control defined elsewhere.} 

-

-        \item{}{\code{min.distance=1}: Numeric scalar. The minimum

-          pixel distance before collapsing range items, only if

-          \code{collapse==TRUE}. See \code{\link{collapsing}} for details.} 

-

-        \item{}{\code{min.height=3}: Numeric scalar. The minimum range

-          height in pixels to display. All ranges are expanded to this

-          size in order to avoid rendering issues. See \code{\link{collapsing}}

-          for details.} 

-

-        \item{}{\code{min.width=1}: Numeric scalar. The minimum range

-          width in pixels to display. All ranges are expanded to this

-          size in order to avoid rendering issues. See \code{\link{collapsing}}

-          for details.} 

-

-        \item{}{\code{reverseStrand=FALSE}: Logical scalar. Set up the

-          plotting coordinates in 3' -> 5' direction if \code{TRUE}.

-          This will effectively mirror the plot on the vertical axis.} 

-

-        \item{}{\code{rotation.title=90}: The rotation angle for the

-          text in the title panel. Even though this can be adjusted,

-          the automatic resizing of the title panel will currently not

-          work, so use at own risk.} 

-

-        \item{}{\code{rotation=0}: The rotation angle for all text

-          unless a more specific definiton exists.} 

-

-        \item{}{\code{showAxis=TRUE}: Boolean controlling whether to

-          plot a y axis (only applies to track types where axes are

-          implemented).} 

-

-        \item{}{\code{showTitle=TRUE}: Boolean controlling whether to

-          plot a title panel. Although this can be set individually

-          for each track, in multi-track plots as created by

-          \code{\link{plotTracks}} there will still be an empty

-          placeholder in case any of the other tracks include a title.

-          The same holds true for axes. Note that the the title panel

-          background color could be set to transparent in order to

-          completely hide it.} 

-

-        \item{}{\code{v=-1}: Integer scalar. Parameter controlling the

-          number of vertical grid lines, see \code{\link{panel.grid}}

-          for details.} 

-

-      } 

-

-    } 

-

   } 

 }