plotSignalTracks

A wrapper around `Gviz` for quick plotting of genomic signals in a single region.

Usage

plotSignalTracks(
  files = list(),
  region,
  ensdb = NULL,
  colors = "darkblue",
  type = "histogram",
  genomeAxis = 0.3,
  extend = 0.15,
  aggregation = c("mean", "median", "sum", "max", "min", "heatmap", "overlay",
    "heatmap+mean"),
  transcripts = c("collapsed", "full", "coding", "none"),
  genes.params = list(col.line = "grey40", col = NULL, fill = "#000000"),
  align.params = list(color = NULL),
  tracks.params = list(),
  extraTracks = list(),
  background.title = "white",
  col.axis = "grey40",
  bed.rotation.title = 0,
  col.title = "black",
  cex.title = 0.65,
  overlay.alpha = 100,
  normFactors = NULL,
  ...
)

Arguments

files

A named list or vector of paths to signal files (e.g. bigwig/bam, but also bed files). If a list, list elements will be overlaid or aggregated (depending on the `aggregation` argument). Formats accepted by DataTrack's `range` argument are also accepted. Can also include `GRanges ` objects (which will be plotted as AnnotationTrack) or objects inheriting the GdObject class (i.e. any `Gviz` track object).

region

A genomic region, either as a `GRanges` object or as a string (i.e. `region="chr5:10000-12000`). Alternatively, if `ensdb` is provided, a gene name can be given, and the gene's coordinates will be used as region.

ensdb

An optional EnsDb object form which to grab transcripts.

colors

Signal color(s); will be recycled for elements of `files`

type

Signal plot type(s); will be recycled for elements of `files`. This is ignored for bed-like files, which are shown as AnnotationTrack. See the `type` options of DataTrack. In addition to these options, the type 'alignments' can be given for bam files, which will display them as AlignmentsTrack.

genomeAxis

Whether to plot a genome axis. Alternatively, a numeric scalar between 0 and 1 can be given, in which case a scale will be plotted of this relative size.

extend

Either an integer or vector of two integers indicating the number of base pairs by which to extent on either side. If `extend`<=1, this will be interpreted as a fraction of the plotted region.

aggregation

Method for aggregation data tracks, one of: 'mean' (default), 'median', 'max', 'overlay', 'heatmap', or 'heatmap+mean'. The latter will create a mean plot of type `type` followed by a heatmap.

transcripts

Whether to show transcripts (reguires `ensdb`) as "full", "collapsed" (default), "coding" (only coding transcripts) or "none". Alternatively, can be a custom GeneRegionTrack object.

genes.params

Named list of parameters passed to GeneRegionTrack.

align.params

Named list of parameters passed to AlignmentsTrack. Only used for plotting bam files with `type="alignments"`.

tracks.params

Named list of parameters passed to DataTrack.

extraTracks

List of extra custom tracks to be plotted.

background.title

The background color of the track titles.

col.axis

The color of the axes.

bed.rotation.title

Rotation for track titles of bed files.

col.title

The color of the track titles.

cex.title

Expension factor for the font size of the track titles.

overlay.alpha

Transparency (0 to 250) when overlaying tracks.

...

Passed to plotTracks.

Value

A list of GenomeGraph tracks to be plotted.

Examples

# fetch path to example bigwig file:
(bw <- system.file("extdata/example_rna.bw", package="epiwraps"))
#> [1] "/home/runner/work/_temp/Library/epiwraps/extdata/example_rna.bw"
plotSignalTracks(list(track1=bw), region="8:22165140-22212326")

# if we had an EnsDb object loaded, we could just input a gene instead of 
# coordinates, and the transcript models would automatically show (not run):
# plotSignalTracks(list(track1=bw), region="BMP1", ensdb=ensdb)
# show all transcript variants:
# plotSignalTracks(list(tracks=bw), region="BMP1", ensdb=ensdb,
#                  transcripts="full")