Package 'TnT'

Composite Track

Description

Two or more arbitrary tracks can be used to create a composite track, by which different features can be shown in the same track.

Usage

## S4 method for signature 'TnTTrack,TnTTrack'
merge(x, y, ...)

## S4 method for signature 'TnTTrack,missing'
merge(x, y, ...)

Arguments

x, y, ...

Track constructed with track-constructors or composite track.

Value

Returns a "CompositeTrack" object.

See Also

http://tnt.marlin.pub/articles/examples/track-CompositeTrack.html

Examples

gr <- GRanges("chr1", IRanges(c(11000, 20000, 60000), width = 2000))
gpos <- GRanges("chr1", IRanges(c(12000, 21000, 61000), width = 1), value = c(1, 2, 3))
btrack <- BlockTrack(gr, label = "Block Track", tooltip = as.data.frame(gr), color = "lightblue4")
ptrack <- PinTrack(gpos, label = "Pin Track", tooltip = as.data.frame(gpos), background = "beige")

ctrack <- merge(btrack, ptrack)
## Not run: 
TnTBoard(ctrack)

## End(Not run)

---

Printing TnTBoard in Rmarkdown

Description

S3 method to automatically render a TnTBoard with knitr.

Usage

## S3 method for class 'TnTBoard'
knit_print(x, ..., options = NULL)

Arguments

x	A TnTBoard or TnTGenome object.
..., options	Passed to htmlwidget:::knit_print.htmlwidget.

Value

htmlwidget:::knit_print.htmlwidget invisibly returns a character vector with "browsable_html" S3 class.

References

knit_print

Examples

track <- BlockTrack(GRanges("chr12", IRanges(c(100, 400, 700), width = 100)),
                    color = c("green", "red", "blue"))
tntboard <- TnTGenome(track)
## Not run: 
knitr::knit_print(tntboard)

## End(Not run)

---

Scale Qualitative Values to Color

Description

A simple util function that scales a factor to color based on the palette function.

Usage

mapcol(value, palette.fun = grDevices::rainbow, ...)

Arguments

value	A factor or character vector that may have n unique values.
palette.fun	The palette function to generate colors. For example, terrain.colors.
...	Extra arguments passed to the palette function.

Value

A character vector as colors, with the same length of value. Same values in value will have the same color.

Examples

mapcol(iris$Species)

---

Range of Tracks

Description

Range of Tracks

Usage

## S4 method for signature 'RangeBasedTrack'
range(x, ..., with.revmap = FALSE, ignore.strand = FALSE, na.rm = FALSE)

## S4 method for signature 'CompositeTrack'
range(x, ..., with.revmap = FALSE, ignore.strand = FALSE, na.rm = FALSE)

Arguments

x	A TnTTrack object.
..., with.revmap, ignore.strand, na.rm	Passed to range,GenomicRanges-method.

Value

Returns a GRanges object.

---

Range of TnTBoard

Description

Get combined range of all tracks in a TnTBoard, used internally.

Usage

## S4 method for signature 'TnTBoard'
range(x, ..., with.revmap = FALSE, ignore.strand = FALSE, na.rm = FALSE)

Arguments

x	TnTBoard.
..., with.revmap, ignore.strand, na.rm	Passed to range,GenomicRanges-method.

Value

GRanges.

---

Save a TnTBoard to an HTML file

Description

A simple wrapper of saveWidget, which saves a TnTBoard/TnTGenome object to an HTML file (e.g. for sharing with others).

Usage

saveTnT(
  tntdef,
  file,
  selfcontained = TRUE,
  libdir = NULL,
  background = "white",
  knitrOptions = list()
)

Arguments

tntdef	A TnTBoard/TnTGenome object to save.
file, selfcontained, libdir, background, knitrOptions	Passed to saveWidget.

Value

Return NULL.

Examples

data <- GRanges("chr2", IRanges(c(6,9,42), width = 1),
                value = c(0.3, 0.5, 0.9))
track <- PinTrack(data, label = NULL, background = "green")
genome <- TnTGenome(list(track))
destfile <- tempfile(fileext = ".html")
destfile
saveTnT(genome, destfile)
## Not run: 
utils::browseURL(destfile)

## End(Not run)

---

Seqinfo of TnTTrack and TnTBoard

Description

Seqinfo of TnTTrack and TnTBoard

Usage

## S4 replacement method for signature 'RangeBasedTrack'
seqinfo(x, new2old = NULL, pruning.mode = c("error", "coarse", "fine", "tidy")) <- value

## S4 method for signature 'RangeBasedTrack'
seqinfo(x)

## S4 method for signature 'RangeBasedTrack'
seqlevelsInUse(x)

## S4 method for signature 'TnTBoard'
seqinfo(x)

## S4 method for signature 'CompositeTrack'
seqinfo(x)

## S4 replacement method for signature 'CompositeTrack'
seqinfo(x, new2old = NULL, pruning.mode = c("error", "coarse", "fine", "tidy")) <- value

## S4 method for signature 'CompositeTrack'
seqlevelsInUse(x)

Arguments

x	A TnTTrack or TnTBoard object.
new2old, pruning.mode, value	Passed to seqinfo method for GenomicRanges.

Value

seqinfo returns a SeqInfo object.

Examples

btrack1 <- BlockTrack(GRanges("chr1", IRanges(1, 123)))
btrack2 <- BlockTrack(GRanges("chr2", IRanges(3, 599)))
ctrack <- merge(btrack1, btrack2)
board <- TnTBoard(list(btrack1, btrack2))

seqinfo(btrack1)
seqinfo(btrack2)
seqinfo(ctrack)
seqinfo(board)

---

Display Labels with Strand

Description

A simple util function that used internally to generate display labels of GeneTrack and TxTrack.

Usage

strandlabel(labels, strands)

Arguments

labels	Character vector, names of each feature.
strands	Factor or character vector with the same length of labels, can be "+", "-" or "*".

Value

A character vector that combines the labels with strand information.

Examples

strandlabel(c("gene1", "gene2", "gene3"), c("+", "-", "*"))

---

Shiny bindings for TnT

Description

Output and render functions for using TnT within Shiny applications and interactive Rmd documents.

Usage

TnTOutput(outputId, width = "100%", height = "auto")

renderTnT(expr, env = parent.frame(), quoted = FALSE)

Arguments

outputId	output variable to read from
width, height	Must be a valid CSS unit (like '100%', '400px', 'auto') or a number, which will be coerced to a string and have 'px' appended.
expr	An expression that generates a TnTBoard/TnTGenome object.
env	The environment in which to evaluate expr.
quoted	Is expr a quoted expression (with quote())? This is useful if you want to save an expression in a variable.

Value

An output or render function that enables the use of the converted htmlwidget within Shiny applications.

Examples

library(shiny)

ui <- fluidPage(fluidRow(
    column(width = 2, {
        "A Simple Example Here"
    }),
    column(width = 10, {
        TnTOutput("out")
    })
))
server <- function (input, output) {
    re.btrack <- reactive({
        gr <- GRanges("chr12", IRanges(100, 1000))
        BlockTrack(gr)
    })
    output$out <- renderTnT({
        TnTBoard(re.btrack())
    })
}
## Not run: 
shinyApp(ui = ui, server = server)

## End(Not run)

---

TnTBoard

Description

A TnTBoard or TnTGenome object stores a list of tracks and can be automatically shown in an interactive R session or in rmarkdown output.

Usage

TnTBoard(
  tracklist,
  view.range = GRanges(),
  coord.range = IRanges(),
  zoom.allow = IRanges(),
  allow.drag = TRUE,
  use.tnt.genome = FALSE
)

TnTGenome(
  tracklist,
  view.range = GRanges(),
  coord.range = IRanges(),
  zoom.allow = IRanges(),
  allow.drag = TRUE
)

Arguments

tracklist	One track or a list of tracks to view.
view.range	Length-one GRanges object, sets the initial view range.
coord.range	Length-one IRanges object or length-two numeric vector, sets the coordinate limit of the board (i.e. minimum/maximum possible coordinate).
zoom.allow	Length-one IRanges object or length-two numeric vector, sets the minimum and maximum extent of the board (i.e. the limit when zooming in and zooming out).
allow.drag	Logical, whether drag should be allowed? Default TRUE.
use.tnt.genome	Logical, whether to add axis and location. 'TnTGenome(...)' is essentially a wrapper to 'TnTBoard(..., use.tnt.genome = TRUE)'.

Value

Returns a TnTBoard or TnTGenome object which has printing method to be rendered as a htmlwidget.

Examples

track <- BlockTrack(GRanges("chr1", IRanges(start = c(100, 300, 500), width = c(10, 100, 200))))
## Not run: 
TnTGenome(track)

## End(Not run)

---

Access Track Tooltips

Description

Access Track Tooltips

Usage

tooltip(x)

tooltip(x) <- value

## S4 method for signature 'TrackData'
tooltip(x)

## S4 method for signature 'TnTTrack'
tooltip(x)

## S4 replacement method for signature 'TrackData,data.frame'
tooltip(x) <- value

## S4 replacement method for signature 'TnTTrack,data.frame'
tooltip(x) <- value

Arguments

x	A TnTTrack object.
value	A data frame to replace, its row number should equal to length of data.

Value

tooltip returns a data frame.

Examples

gr <- GRanges("chr12", IRanges(c(6, 69), c(42, 135)), Name = c("my range 1", "my range 2"))
track <- BlockTrack(gr)
tooltip(track)
tooltip(track)$Width <- width(gr)
tooltip(track)

---

Track Constructors

Description

Track Constructors

Usage

BlockTrack(
  range,
  label = deparse(substitute(range)),
  tooltip = mcols(range),
  color = "blue",
  background = NULL,
  height = 30
)

VlineTrack(
  pos,
  label = deparse(substitute(pos)),
  tooltip = mcols(pos),
  color = "green",
  background = NULL,
  height = 40
)

PinTrack(
  pos,
  value = mcols(pos)$value,
  domain = numeric(),
  label = deparse(substitute(pos)),
  tooltip = mcols(pos),
  color = "red",
  background = NULL,
  height = 40
)

LineTrack(
  pos,
  value = mcols(pos)$value,
  domain = numeric(),
  label = deparse(substitute(pos)),
  color = "yellow",
  background = NULL,
  height = 70
)

AreaTrack(
  pos,
  value = mcols(pos)$value,
  domain = numeric(),
  label = deparse(substitute(pos)),
  color = "pink",
  background = NULL,
  height = 70
)

GeneTrackFromTxDb(
  txdb,
  seqlevel = seqlevels(txdb),
  label = deparse(substitute(txdb)),
  color = "black",
  background = NULL,
  height = 100
)

FeatureTrack(
  range,
  label = deparse(substitute(range)),
  tooltip = mcols(range),
  names = base::names(range),
  color = "black",
  background = NULL,
  height = 200
)

GroupFeatureTrack(
  grl,
  label = deparse(substitute(grl)),
  tooltip = mcols(grl),
  names = base::names(grl),
  color = "black",
  background = NULL,
  height = 200
)

TxTrackFromTxDb(
  txdb,
  seqlevel = seqlevels(txdb),
  label = deparse(substitute(txdb)),
  color = "red",
  background = NULL,
  height = 300
)

TxTrackFromGRanges(
  gr,
  label = deparse(substitute(gr)),
  color = "red",
  background = NULL,
  height = 300
)

Arguments

range, pos	GRanges or IRanges object. For pos, all the width should be one.
label	Character, shown as label of the track on the left, could be NULL.
tooltip	A data frame that is parallel to range or pos.
color	Character vector or integer vector that sets the color of the features. It can be color names, hexadecimal string or positive integer i meaning palette()[i], as described in col2rgb. It can be parallel to the data (i.e. have the same length) thus sets colors of each individual feature.
background	Length-one character vector that sets background of the track, could be NULL.
height	Length-one numeric vector that sets height of the track.
value, domain	'value' is a numeric vector that is parallel to pos, which indicates height of features at each position for PinTrack, LineTrack and AreaTrack. 'domain' is a length-two numeric vector which sets the lower and upper limit of 'value' (i.e. the limit on y-axis).
txdb, seqlevel	The TxDb and seqlevel to extract gene or transcript from.
names	Character vector with the same length of data, which is used to generate display labels shown together with features when zooming in.
grl	For 'GroupFeatureTrack' function, a GRangesList object that represents grouped ranges as data source. It is assumed that ranges in each group are on the same strand and do not overlap.
gr	For 'TxTrackFromGRanges' function, a GRanges object that represents exons and cds as data source, and will be rendered as transcripts. Two meta-columns ("type", "tx_id") are required, "type" can be "exon" or "cds" by which ranges of "cds" will be filled with color, "tx_id" indicates the grouping.

Value

Returns an object that extends "TnTTrack" class.

See Also

You can find various examples at http://tnt.marlin.pub/articles/examples/, also see composite-track on how to create a composite track.

Examples

BlockTrack(range = GRanges("chr1", IRanges(199, 4000)),
           color = "green", background = "red", height = 100)

---

Access Track Data

Description

Access and modify the track data. x$name and x$name <- value are just shortcuts for trackData(x)$name and trackData(x)$name <- value, respectively.

Usage

trackData(x)

trackData(x) <- value

## S4 method for signature 'TnTTrack'
x$name

## S4 replacement method for signature 'TnTTrack'
x$name <- value

Arguments

x	A TnTTrack object.
value	Replaced value.
name	Passed to the inner method for track data.

Value

trackData on all track types except "CompositeTrack" returns an object that inherits GRanges class, which means they should behave like a GRanges. While trackData on "CompositeTrack" returns a list of tracks.

Examples

track <- BlockTrack(GRanges("chr1", IRanges(6, 54)))
class(trackData(track)) # track data of block track is an object that inherits GRanges.
#trackData(track)
ctrack <- merge(track, track)
class(trackData(ctrack)) # track data of composite track is a list of tracks
#trackData(ctrack)

---

Track List in TnTBoard

Description

The tracks of a TnTBoard are stored as a list which can be accessed or modified with these functions.

Usage

tracklist(tntboard)

tracklist(tntboard) <- value

Arguments

tntboard	A TnTBoard or TnTGenome object
value	A list of tracks

Value

tracklist returns a list of tracks.

Examples

bt <- BlockTrack(GRanges("chr21", IRanges(100, 1200)))
li.tracks <- list(bt, bt)
board <- TnTBoard(li.tracks)
tracklist(board)
## Not run: 
show(board)

## End(Not run)
tracklist(board) <- list(bt)
## Not run: 
show(board)

## End(Not run)

---

Track Spec

Description

Height, background and label are common options of all tracks, use these functions to get and set them.

Usage

trackSpec(track, which = c("background", "height", "label"))

trackSpec(track, which = c("background", "height", "label")) <- value

Arguments

track	A TnTTrack object.
which	Character vector, can be "background", "height" or "label".
value	Value to set: background should be character, height should be numeric, label should be character. If length of which is bigger than one, value should be a list with the same length.

Value

For trackSpec, if length of which equals to one, return a scalar character or numeric, if length of which is bigger than one, return as a list.

Examples

track <- BlockTrack(GRanges("chr13", IRanges(6, 9)))
trackSpec(track, "background")
trackSpec(track, c("height", "label"))
trackSpec(track, c("height", "label")) <- list(100, "my range")
trackSpec(track, "background") <- "green"
trackSpec(track)

---

Convert a TnTBoard to htmlwidget

Description

This function is only provided for users who are familiar with the concept of htmlwidgets-package. It explicitly convets a TnTBoard or TnTGenome object to a htmlwidget object. You do not need it in most cases.

Usage

trackWidget(tntdef, elementId = NULL)

Arguments

tntdef	A TnTBoard/TnTGenome object or a htmlwidget object. If it is a htmlwidget object, the function will return it as is.
elementId	An id for the htmlwidget (random by default).

Value

The function returns a htmlwidget object.

Examples

b <- TnTBoard(BlockTrack(GRanges("chr12", IRanges(1, 123))))
widget <- trackWidget(b)
class(widget)
identical(widget, trackWidget(widget))

---