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)

Arguments

range, pos GRanges or IRanges object. For pos, all the width should be one. Character, shown as label of the track on the left, could be NULL. A data frame that is parallel to range or pos. 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. Length-one character vector that sets background of the track, could be NULL. Length-one numeric vector that sets height of the track. 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). The TxDb and seqlevel to extract gene or transcript from. Character vector with the same length of data, which is used to generate display labels shown together with features when zooming in. 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. 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.

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)#> A BlockTrack
#> | Label:	GRanges("chr1", IRanges(199, 4000))
#> | Background:	red
#> | Height:	100
#> | Data:	RangeTrackData object with 1 range and 3 metadata columns:
#> |        seqnames      ranges strand |      tooltip       color       key
#> |           <Rle>   <IRanges>  <Rle> | <data.frame> <character> <integer>
#> |    [1]     chr1 [199, 4000]      * |                    green         1
#> |    -------
#> |    seqinfo: 1 sequence from an unspecified genome; no seqlengths