track-constructors: Track Constructors

In Marlin-Na/TnT: Interactive Visualization for Genomic Features

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)

Marlin-Na/TnT documentation built on Sept. 15, 2024, 5:27 a.m.