track-constructors: Track Constructors

Description Usage Arguments Value See Also Examples

Description

Track Constructors

Usage

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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

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

TnT documentation built on Nov. 8, 2020, 8:11 p.m.