tracks: 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.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.width

track labeling size.

Value

A Tracks object.

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.

Examples

Run this code

## 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 <- ggbio:::get_gtable(tks)
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"))