track-constructors: Track Constructors
In TnT: Interactive Visualization for Genomic Features

Description Usage Arguments Value See Also Examples

Track Constructors

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
)

`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.