gTrack-class: Construct a new 'gTrack'

In mskilab/gTrack: Plotting multiple tracks of complex genomic data across multiple genomic windows

Construct a new gTrack

Description

S4 class for gTrack

Class gTrack defines a subsettable object that wraps formatting information around genomic data (GRanges, GRangesList, RleLists, UCSC formats, ffTrack) and can be displayed in a "genome browser" style plot.

Arguments described as "formatting" are vectors. They are replicated (if necessary) to match the length of the object.

Usage

gTrack(
  data = NULL,
  y.field = NA,
  mdata = NULL,
  edges = NULL,
  vars = NULL,
  colormaps = NULL,
  height = 10,
  ygap = 2,
  ylab = "",
  stack.gap = 0,
  cex.label = 1,
  gr.cex.label = cex.label * 0.8,
  gr.srt.label = 0,
  col = NA,
  border = NA,
  angle = 15,
  name = "",
  gr.colorfield = NA,
  y.quantile = 0.01,
  y.cap = T,
  lwd.border = 1,
  hadj.label = 1,
  vadj.label = 0.5,
  smooth = NA,
  round = NA,
  ywid = NA,
  ypad = 0,
  seqinfo = NA,
  circles = FALSE,
  lines = FALSE,
  bars = FALSE,
  draw.paths = FALSE,
  path.col = "black",
  path.lwd = 1,
  draw.var = FALSE,
  triangle = !is.null(mdata),
  max.ranges = 50000,
  source.file.chrsub = T,
  y0.bar = NA,
  yaxis = !is.na(y.field),
  yaxis.pretty = 5,
  yaxis.cex = 1,
  chr.sub = TRUE,
  edgevars = NA,
  gr.labelfield = NA,
  grl.labelfield = NA,
  grl.colorfield = NA,
  grl.cexfield = NA,
  xaxis.prefix = "",
  xaxis.unit = 1,
  xaxis.suffix = "",
  xaxis.round = 3,
  xaxis.cex.label = 1,
  xaxis.newline = TRUE,
  xaxis.chronly = FALSE,
  xaxis.width = TRUE,
  xaxis.interval = "auto",
  xaxis.label.angle = 0,
  xaxis.ticklen = 1,
  xaxis.cex.tick = 1,
  sep.lty = 2,
  sep.lwd = 1,
  sep.bg.col = "gray95",
  sep.draw = TRUE,
  y0 = NA,
  y1 = NA,
  m.sep.lwd = 1,
  cmap.min = NA,
  cmap.max = NA,
  labels.suppress = FALSE,
  labels.suppress.grl = labels.suppress,
  labels.suppress.gr = labels.suppress,
  bg.col = "white",
  formatting = NA
)

Arguments

data	Instance of one of the following objects: (1) GRanges (2) GRangesList (3) ffTrack or (4) character representing Bed, Wig, BigWig, or .rds GRanges file. It can also be a list of the above (if specifying multiplying tracks.
y.field	vector or scalar character referencing meta data field of GRanges or GRangesList to use for "y axis" coordinate when plotting numeric tracks, (note: for a RleList or ffTrack this field is automatically set to "score"), default is NA for non-numeric tracks
mdata	Square matrix representing values at connections between genomic elements (e.g. chr8:1,000-2,000 to chr3:5,000-6,000). The number of rows (and thus columns) must be equal to the length of the data element. The value of the (i,j) element of this matrix represents a value for the intersection of data[i] and data[j]. Note that all connections are assumed to be symmetric, and only the upper triangle will be read. Displays a warning if the matrix is non-symmetric
edges	Data frame of columns $from, $to, and optional fields $col, $lwd, and $lty, specifying edges linking data items. Also can be a list of the above if specifying multiple tracks (and must be compatible in length with data arg)
colormaps	length(.Object) length named list of named vectors whose entry i maps uniques value of a data field to colors. The data.field is specified by the name of the list entry, and the unique values / colors are specified by the named vector.
height	vector or scalar numeric specifying height of track(s) (in relative units)
ygap	vector or scalar numeric specifying gap between tracks
stack.gap	vector or scalar.numeric specifying x gap between stacking non-numeric GRanges or GrangesLists items in track(s)
cex.label	vector or scalar numeric specifying the expansion factor of the range labels (formatting)
gr.cex.label	vector or scalar numeric specifying GRanges label character expansion (default is cex.label) (formatting)
gr.srt.label	vector or scalar numeric between 0 and 180 specifying rotation of GRanges labels (formatting)
col	vector or scalar character specifying static color for track(s), if NA then color is specified by colormaps() property or gr.colorfield or col meta data field of GRanges / GRangesList data object
border	vector or scalar character specifying static border for polygons in track(s), if NA then $border is determine duing gr.colorfield / colormap or meta field $border of GRanges / GRangesList
angle	vector of scalar numeric specifying angle of polygons that represent signed range' items (only relevant if used within chainedTracks object)
name	vector or scalar character specifying name of this track, which will be displayed on label to the left of the track
lwd.border	vector or scalar integer specifying the thickness of the polygon borders (formatting)
hadj.label	vector or scalar numeric specifying the horizontal adjustment of the range labels (formatting)
vadj.label	vector or scalar numeric specifying the vertical adjustment of the range labels (formatting)
ywid	vector or scalar numeric specifying the y-extent of individual ranges (in local plot coordinates)
ypad	vector or scalar numeric between 0 and 1 specifying how much whitespace padding to add within panel (formatting)
circles	vector or scalar logical specifying whether to scatter plot range data (formatting)
lines	vector or scalar logical specifying whether to line plot range data (formatting)
bars	vector or scalar logical specifying whether to bar plot range data (formatting)
draw.paths	vector or scalar logical specifying whether to interpret GRangesLists as "paths" and connect them with a a set of spline curves. (formatting)
path.col	vector or scalar character specifying color of path (only applicable for tracks in which draw.paths = T) (formatting)
draw.var	vector or scalar logical specifying whether to draw.var for GRanges / GRangesList specifying reads (GRanges must contain $cigar +/- $MD field) (formatting)
max.ranges	vector or scalar numeric specifying what is the max number of ranges to plot in a window (formatting)
source.file.chrsub	vector or scalar logical specifying whether or not sub "chr" out of any external files (e.g. UCSC style files) (formatting)
y0.bar	vector or scalar numeric specifying where to draw the lower boundary of a bar in a bar plot (only applicable if bars == T) (formatting)
yaxis	vector or scalar logical specifying whether to print yaxis (formatting)
yaxis.pretty	vector or scalar positive integer specifying how many ticks to optimally draw on yaxis (formatting)
gr.labelfield	vector or scalar character specifying which GRanges meta data field to use for GRanges label (default "label") (formatting)
grl.labelfield	vector or scalar character specifying which GRanges meta data field to use for GRangesList label (default "label") (formatting)
grl.colorfield	vector or scalar character specifying which GRanges meta data field to use for GRangesList labels color (default "label.color") (formatting)
grl.cexfield	vector or scalar character specifying which GRanges meta data field to use for GRangesList labels cex (default "cex.label") (formatting)
xaxis.unit	vector or scalar numeric specifying the unit that will be used in describing x axis coordinates (TODO: move to display) (formatting)
xaxis.suffix	vector or scalar numeric specifying the suffix that will be used in describin x axis coordinates (TODO: move to display) (formatting)
xaxis.round	vector or scalar non-neg integer specifying number of decimals to round xaxis coordinate labels (formatting)
xaxis.newline	vector or scalar logical specifying whether to draw a newline in the xaxis coordinate labels (formatting)
xaxis.width	Logical scalar specifying whether to add window width to xaxis window labels [TRUE]
xaxis.label.angle	vector or scalar numeric between 0 and 360 specifying angle with which to draw xaxis coordinate labels (formatting)
xaxis.ticklen	Scalar numeric specifying lengths for axis ticks (formatting)
xaxis.cex.tick	Scalar numeric specifying expansion factor for axis tick labels (formatting)
sep.lty	Scalar integer specifying line style for window separators [2] (dashed line)
sep.lwd	Scalar numeric specifying line thickness for window separators [1]
sep.bg.col	Color (supplied by name or hex code) for the background of the windows [gray95]
sep.draw	Logical allowing separators to be turned off [FALSE]
cmap.min	minimum saturating data value of color map for triangle plot
cmap.max	maximum saturating data value of color map for triangle plot
labels.suppress	whether to suppress labels (both GRangesList and GRanges)
labels.suppress.gr	whether to suppress GRangesList labels
legend.maxitems	Scalar positive integer specifying what is the maximum number of items to include in legend [Inf]
label.suppress	vector or scalar logical flag specifying whether to suppress all GRanges / GRangesList label drawing (formatting)
label.suppress.gr	vector or scalar logical flag specifying whether to suppress GRanges label drawing (formatting)
label.suppress.grl	vector or scalar logical flag specifying whether to suppress GRangesList label drawing (formatting)
cex.label.gr	size of bottom level label (i.e. GRanges in a GrangesListitem, e.g. exons in a gene)
split	vector or scalar logical flag specifying whether to split when lifting (only relevant if used wihtin chainedTracks object)
xaxis.nticks	vector or scalar positive integer specifying how many xaxis ticks to optimally draw (formatting)
y.grid.col	vector or scalar character specifying color of "gridlines" used to specify numeric track data (formatting)
y.grid.cex	vector or scalar non-neg numeric specifying character expansion for y tick / y grid labels (formatting)
y.grid.lty	vector or scalar positive integer specifying line style of y grid lines for numeric tracks (formatting)
y.grid.lwd	vector or scalar positive integer specifying thickness of y grid lines for numeric tracks (formatting)
y.grid.labx	vector or scalar positive integer specifying fraction of xlim left of plot to place y axis labels (formatting)
path.col.arrow	vector or scalar character specifying color of arrow of path (only applicable for tracks in which draw.paths = T) (formatting)
path.cex.arrow	vector or scalar numeric > 0 specifying expansion factor of arrow of path (only applicable for tracks in which draw.paths = T) (formatting)
path.stack.y.gap	vector or scalar numeric > 0 specifying y stack gap of paths (only applicable for tracks in which draw.paths = T) (formatting)
path.stack.x.gap	vector or scalar numeric > 0 specifying x stack gap for paths (only applicable for tracks in which draw.paths = T) (formatting)
path.cex.v	vector or scalar numeric > 0 specifying vertical bulge of sline in paths (only applicable for tracks in which draw.paths = T) (formatting)
path.cex.h	vector or scalar numeric > 0 specifying horizontal bulge of spline in paths (formatting) (only applicable for tracks in which draw.paths = T) (formatting)
draw.backbone	vector or scalar logical specifying whether to draw "backbone" connecting different items in a GRangesList item (formatting)
...	additional formatting arguments to gTrack

Slots

data

length(.Object) length list containing genomic data (e.g. GRanges, GrangesLists, RleLists, path to ucsc file or ffTrack file on disk)

seqinfo

Seqinfo object

colormap

length(.Object) length named list of named vectors whose entry i specifies the colormap for the meta data field of object entry i (specified by the name) and maps unique value of that data field to colors (specified by the named vector)

edges

list of data.frames of length length(.Object) which has columns $from, $to, and optional fields $col, $lwd, and $lty to specify splined edges joining data items in the corresponding track

formatting

data.frame holding all of the formatting options

mdata

matrix holding interaction data between genomic loci (e.g. hiC)

vars

List of variants associated with track

Author(s)

Marcin Imielinski

mskilab/gTrack documentation built on Aug. 17, 2024, 6:10 a.m.