track-constructors {TnT} | R Documentation |
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 |
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. |
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.
BlockTrack(range = GRanges("chr1", IRanges(199, 4000)), color = "green", background = "red", height = 100)