tracks {ggbio} | R Documentation |
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.
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"))
... |
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 |
|
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. |
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.
A Tracks
object.
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.
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.
obj
is the Tracks object, this reset the tracks back to
original or backuped version.
obj
is the Tracks object, this clear previous backup and
use current setting for a new backup.
Tengfei Yin
## 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"))