plotTracks {Gviz} | R Documentation

## The main plotting function for one or several GenomeGraph tracks.

### Description

`plotTracks` is the main interface when plotting single track objects, or lists of tracks linked together across the same genomic coordinates. Essentially, the resulting plots are very similar to the graphical output of the UCSC Genome Browser, execpt for all of the interactivity.

### Usage

    plotTracks(trackList, from=NULL, to=NULL, ..., sizes=NULL,
    panel.only=FALSE, extend.right=0, extend.left=0, title.width=NULL,
    add=FALSE, main, cex.main=2, fontface.main=2, col.main="black",
    margin=6, chromosome=NULL, innerMargin=3)

### Arguments

`trackList` | A list of GenomeGraph track objects, all inheriting from class `GdObject`. The tracks will all be drawn to the same genomic coordinates, either as defined by the `from` and `to` arguments if supplied, or by the maximum range across all individual items in the list.
`from, to` | Charactar scalar, giving the range of genomic coordinates to draw the tracks in. Note that `to` cannot be larger than `from`. If `NULL`, the plotting ranges are derived from the individual tracks. See `extend.left` and `extend.right` below for the definition of the final plotting ranges.
`...` | Additional arguments which are all interpreted as display parameters to tweak the appearance of the plot. These parameters are global, meaning that they will be used for all tracks in the list where they actually make sense, and they override the track-internal settings. See `settings` for details on display parameters.
`sizes` | A numeric vector of relative vertical sizes for the individual tracks of lenght equal to the number of tracks in `trackList`, or `NULL` to auto-detect the most appropriate vertical size proportions.
`panel.only` | Logical flag, causing the tracks to be plotted as lattice-like panel functions without resetting the plotting canvas and omitting the title pane. This allows to embed tracks into a trellis layout. Usually the function is called for a single track only when `panel.only==TRUE`.
`extend.right, extend.left` | Numeric scalar, extend the plotting range to the right or to the left by a fixed number of bases. The final plotting range is defined as `from-extend.left` to `to+extend.right`.
`title.width` | A expansion factor for the width of the title panels. This can be used to make more space, e.g. to accomodate for more detailed data axes. The default is to use as much space as needed to fit all the annotation text.
`add` | Logical flag, add the plot to an existing plotting canvas without re-initialising.
`main` | Character scalar, the plots main header.
`cex.main, fontface.main,col.main` | The fontface, color and expansion factor settings for the main header.
`margin` | The margin width to add to the plot in pixels.
`innerMargin` | The inner margin width to add to the plot in pixels.
`chromosome` | Set the chromosome for all the tracks in the track list.

### Details

GenomeGraph tracks are plotted in a vertically stacked layout. Each track panel is split up into a title section containing the track name, as well as an optional axis for tracks containing numeric data, and a data section showing the actual data along genomic coordinates. In that sense, the output is very similar to the UCSC Genome Browser.

The layout of the individual tracks is highly customizable though so called "display parameters". See `settings` for details.

While plotting a track, the software automatically computes HTML image map coordinates based on the current graphics device. These coordinates as well as the associated annotation information can later be used to embed images of the plots in semi-interactive HTML pages. See `ImageMap` for details.

### Value

A list of GenomeGraph tracks, each one augmented by the computed image map coordinates in the `imageMap` slot, along with the additional `ImageMap` object `titles` containing information about the title panels.

### Author(s)

Florian Hahne

### See Also

`GdObject`

`ImageMap`

`RangeTrack`

`StackedTrack`

`settings`

### Examples

    ## Create some tracks to plot
    st <- c(2000000, 2070000, 2100000, 2160000)
    ed <- c(2050000, 2130000, 2150000, 2170000)
    str <- c("-", "+", "-", "-")
    gr <- c("Group1","Group2","Group1", "Group3")
    annTrack <- AnnotationTrack(start=st, end=ed, strand=str, chromosome=7,
                                genome="hg19", feature="test", group=gr,
                                id=paste("annTrack item", 1:4),
                                name="annotation track foo",
                                stacking="squish")

    ax <- GenomeAxisTrack()

    dt <- DataTrack(start=seq(min(st), max(ed), len=10), width=18000,
    data=matrix(runif(40), nrow=4), genome="hg19", chromosome=7,
    type="histogram", name="data track bar")

    ## Now plot the tracks
    res <- plotTracks(list(ax, annTrack, dt))

    ## Plot only a subrange
    res <- plotTracks(list(ax, annTrack, dt), from=2080000, to=2156000)

    ## Extend plotting ranges
    res <- plotTracks(list(ax, annTrack, dt), extend.left=200000, extend.right=200000)

    ## Add a header
    res <- plotTracks(list(ax, annTrack, dt), main="A GenomGraphs plot",
    col.main="darkgray")

    ## Change vertical size and title width
    res <- plotTracks(list(ax, annTrack, dt), sizes=c(1,1,5))

    names(annTrack) <- "foo"
    res <- plotTracks(list(ax, annTrack), title.width=0.6)

    ## Adding and lattice like plots
    library(grid)
    grid.newpage()
    pushViewport(viewport(height=0.5, y=1, just="top"))
    grid.rect()
    plotTracks(annTrack, add=TRUE)
    popViewport(1)
    pushViewport(viewport(height=0.5, y=0, just="bottom"))
    grid.rect()
    plotTracks(dt, add=TRUE)
    popViewport(1)

    ## Not run:
    library(lattice)
    myPanel <- function(x, ...) plotTracks(annTrack, panel.only=TRUE,
    from=min(x), to=max(x), shape="box")
    a <- seq(1900000, 2250000, len=40)
    xyplot(b~a|c, data.frame(a=a, b=1, c=cut(a, 4)), panel=myPanel,
    scales=list(x="free"))

    ## End(Not run)

[Package Gviz version 1.36.2 Index]