tracks {ggbio} | R Documentation

## Tracks for genomic graphics

### Description

`tracks` is a conventient constructor for bindind graphics as trakcs. You dont' have to worry about adjusting different graphics, `tracks` did that for you. It's NOT just limited to bind genomic tracks, you can use this function to bind any tracks with the same defination of x axis, for example, sets of time series plots you made.

Tracks view is most common way to viewing genome features and annotation data and widely used by most genome browsers. Our assumption is that, most graphics you made with ggbio or by yourself using ggplot2, are almost always sitting on the genomic coordinates or the same x axis. And to compare annotation information along with genome features, we need to align those plots on exactly the same x axis in order to form your hypothesis. This function leaves you the flexibility to construct each tracks separately with worrying your alignments later.

### Usage

    tracks(..., heights, xlim, xlab = NULL, main = NULL,
                title = NULL, theme = NULL,
                track.plot.color = NULL,
                track.bg.color = NULL,
                main.height = unit(1.5, "lines"),
                scale.height = unit(1, "lines"),
                xlab.height = unit(1.5, "lines"),
                padding = unit(-1, "lines"),
                label.bg.color =  "white",
                label.bg.fill = "gray80",
                label.text.color = "black",
                label.text.cex = 1,
                label.text.angle = 90,
                label.width = unit(2.5, "lines"))

### Arguments

`...` | plots of class ggplot, generated from ggplot2 or ggbio.
`heights` | numeric vector of the same length of passed graphic object to indicate the ratio of each track.
`xlim` | limits on x. could be `IRanges`, `GRanges`, `numeric` value
`xlab` | label for x axis.
`main` | title for the tracks.
`title` | title for the tracks, alias like main.
`theme` | theme object used for building tracks, this will set to default, which could be reseted later.
`track.plot.color` | Vector of characters of length 1 or the same length of passed plots, background color for each track, default is white.
`track.bg.color` | background color for the whole tracks.
`main.height` | unit. Height to control the title track height.
`scale.height` | unit. Height to control the scale track height.
`xlab.height` | unit. Height to control the xlab track height.
`padding` | single numeric value or unit, if numeric value, the unit would be "lines" by default.
`label.bg.color` | track labeling background rectangle border color.
`label.bg.fill` | track labeling background fill color.
`label.text.color` | track labeling text color.
`label.text.cex` | track labeling text size.
`label.text.angle` | angle to rotate the track labels.
`label.width` | track labeling size.

### Details

`tracks` did following modification for passed plots.

- remove x-axis, ticks, xlab and tile for each track and add scales at bottom. We suppose a new xlab and title would be provided by the `tracks` function for the whole tracks, but we still keep individual's y axis.

- align x-scale limits to make sure every plots sitting on exactly the same x scale.

- squeezing plots together to some extent.

- labeling tracks if names are provided, please check utilities section about `labeled` method.

- return a track object. This would allow many features introduced in this manual.

### Value

A `Tracks` object.

### Track class

constructor `tracks` will return a Tracks object, which has following slots.

`grobs`

  a `ggplotGrobList` object contains a list of `ggplot` object, which is our passed graphics.

`backup`

  a backup of all the slots for holding the original tracks, so users could edit it and reset it back at any time later, and `backup` method will reset the backupped copy.

`ylim`

  y limits for each plot.

`labeled`

  vector of logical value indicates whether a track is labeled or not, for `labeled` attributes please check utilities section.

`mutable`

  vector of logical value indicates whether a track is mutable for theme editing or not, for `mutable` attributes please check utilities section.

`hasAxis`

  vector of logical value indicates whether a track has axis or not, for `hasAxis` attributes please check utilities section.

`heights, xlim, xlab, main, title, theme, fixed, track.plot.color, track.bg.color, main.height, scale.height, xlab.height, padding, label.bg.color, label.bg.fill, label.text.color, label.text.cex, label.text.angle, label.width`

  those slots are described in arguments section for constructor.

### Utilities

Please check examples for usage.

`summary(object)`

  summary information about tracks object.

`fixed(x)`, `fixed(x) <- value`

  `x` is the ggplot object, this controls if a track has a fixed x scale or not, if the `fixed` attributes is `TRUE`, then when you pass this plot to a tracks, this plot won't be re-aligned with other tracks and will keep the original x-axis, this allow you to pass some plot like ideogram. `fixed` function will return a logical value

`labeled(x), labeled(x) <- value`

  `x` is the ggplot object, if you pass named graphics into `tracks`, it will create the labels on the left for you. Several ways supported to name it. You can pass a list of graphics with names. Or you can use `tracks('name1' = p1, 'name 2' = p2, ...)` with quotes for complicated words or simply `tracks(part1 = p1, part = p2, ...)`.

`mutable(x), mutable(x) <- value`

  `x` is the ggplot object, this controls whether a plot in the tracks mutable to theme changing or not, when you use `+` method for Tracks object, add-on edit will only be applied to the the mutable plots.

`bgColor(x), bgColor(x) <- value`

  `x` is the ggplot object, this change the background color for single plot shown in the tracks.

`xlim(x), xlim(x) <- value`

  when `x` is the numeric value, it calls ggplot2::coord_cartesian(xlim = ...) method, we doesn't use ggplot2::xlim() for the reason it will cut data outside the range, and we believe the best behavior would be zoom-in/out like most browser. when `x` is `IRanges`, `GRanges`, it get the range and passed to ggplot2::coord_cartesian function.

  when `x` is Tracks object, `xlim(x)` will return x limits for that tracks. `xlim(x) <- value` replace method only works for Tracks object. `value` could be `numeric`, `IRanges`, `GRanges` object. This will change the x limits associated with tracks.

  `+ xlim(obj)`:`obj` is the numeric range, or `IRanges`, `GRanges` object.

  `+ coord_cartesian()`: please read manual in ggplot2, this controls both xlim an ylim, only accept numerical range.

`+`

  The most nice features about `Tracks` object is the one inherited from ggplot2's components additive features, with `+` method you can use any `theme` object and utilities in ggplot2 package, to add them on a `Tracks` object, for example, if x is our `Tracks` object, `x + theme` would apply theme to any plots in the tracks except those are immutable.

`as(x, "grob")`

  Coerces a Tracks object to a grob for embedding in a larger figure.

### Backup and reset

reset(obj)

  `obj` is the Tracks object, this reset the tracks back to original or backuped version.

backup(obj)

  `obj` is the Tracks object, this clear previous backup and use current setting for a new backup.

### Author(s)

Tengfei Yin

### See Also

`align.plots`

### Examples

    ## make a simulated time series data set
    df1 <- data.frame(time = 1:100, score = sin((1:100)/20)*10)
    p1 <- qplot(data = df1, x = time, y = score, geom = "line")
    df2 <- data.frame(time = 30:120, score = sin((30:120)/20)*10, value = rnorm(120-30 + 1))
    p2 <- ggplot(data = df2, aes(x = time, y = score)) +
      geom_line() + geom_point(size = 4, aes(color = value))
    ## check p2
    p1
    ## check p2
    p2

    ## binding
    tracks(p1, p2)

    ## or
    tks <- tracks(p1, p2)
    tks

    ## combine
    c(tks, tks)
    tks + tks

    cbind(tks, tks)
    rbind(tks, tks) ## different wth c()!
    library(grid)
    x <- as(tks, "grob")
    grid.draw(cbind(x, x))

    ## labeling: default labeling a named graphic
    ## simply pass a name with it
    tracks(time1 = p1, time2 = p2)
    ## or pass a named list with it
    lst <- list(time1 = p1, time2 = p2)
    tracks(lst)

    ## more complicated case please use quotes
    tracks(time1 = p1, "second time" = p2)

    ## set heights
    tracks(time1 = p1, time2 = p2, heights = c(1, 3))

    ## if you want to disable label arbitrarily
    ## default label is always TRUE
    labeled(p2)
    labeled(p2) <- FALSE
    ## set labeled to FALSE, remove label even the plot has a name
    tracks(time1 = p1, time2 = p2)
    labeled(p2) <- TRUE

    ## fix a plot, not synchronize with other plots
    p3 <- p1
    ## default is always FALSE
    fixed(p3)
    ## set to TRUE
    fixed(p3) <- TRUE
    fixed(p3)

    tracks(time1 = p1, time2 = p2, "time3(fixed)" = p3)

    fixed(p3) <- FALSE
    ## otherwise you could run

    ## control axis
    hasAxis(p1)
    hasAxis(p1) <- TRUE
    # ready for weird looking
    tracks(time1 = p1, time2 = p2)
    # set it back
    hasAxis(p1) <- FALSE

    ## mutable
    mutable(p1)
    tracks(time1 = p1, time2 = p2) + theme_bw()
    mutable(p1) <- FALSE
    # mutable for "+" method
    tracks(time1 = p1, time2 = p2) + theme_bw()
    mutable(p1) <- TRUE

    ## bgColor
    bgColor(p1)
    tracks(time1 = p1, time2 = p2)
    bgColor(p1) <- "brown"
    # mutable for "+" method
    tracks(time1 = p1, time2 = p2)
    # set it back
    bgColor(p1) <- "white"

    ## apply a theme to each track
    tks <- tracks(time1 = p1, time2 = p2) + theme_bw()
    tks
    reset(tks)

    ## store it with tracks
    tks <- tracks(time1 = p1, time2 = p2, theme = theme_bw())
    tks
    tks <- tks + theme_gray()
    tks
    ## reset will be introduced later
    reset(tks)

    ## apply a pre-defiend theme for tracks!
    tracks(time1 = p1, time2 = p2) + theme_tracks_sunset()
     tracks(p1, p2) + theme_tracks_sunset()

    ## change limits
    tracks(time1 = p1, time2 = p2) + xlim(c(1, 40))
    tracks(time1 = p1, time2 = p2) + xlim(1, 40)
    tracks(time1 = p1, time2 = p2) + coord_cartesian(xlim = c(1, 40))
    # change y
    tracks(time1 = p1, time2 = p2) + xlim(1, 40) + ylim(0, 10)
    library(GenomicRanges)
    gr <- GRanges("chr", IRanges(1, 40))
    # GRanges
    tracks(time1 = p1, time2 = p2) + xlim(gr)
    # IRanges
    tracks(time1 = p1, time2 = p2) + xlim(ranges(gr))
    tks <- tracks(time1 = p1, time2 = p2)
    xlim(tks)
    xlim(tks) <- c(1, 35)
    xlim(tks) <- gr
    xlim(tks) <- ranges(gr)

    ## xlab, title
    tracks(time1 = p1, time2 = p2, xlab = "time")
    tracks(time1 = p1, time2 = p2, main = "title")
    tracks(time1 = p1, time2 = p2, title = "title")
    tracks(time1 = p1, time2 = p2, xlab = "time", title = "title") + theme_tracks_sunset()

    ## backup and restore
    tks <- tracks(time1 = p1, time2 = p2)
    tks
    tks <- tks + xlim(1, 40)
    tks
    reset(tks)
    tks <- tks + xlim(1, 40)
    tks
    tks <- backup(tks)
    tks <- tks + theme_bw()
    tks
    reset(tks)

    ## padding(need to be fixed for more delicate control)
    tracks(time1 = p1, time2 = p2, padding = 2)

    ## track color
    tracks(time1 = p1, time2 = p2, track.bg.color = "yellow")
    tracks(time1 = p1, time2 = p2, track.plot.color = c("yellow", "brown"))

[Package ggbio version 1.38.0 Index]