plotSignalTracks: plotSignalTracks

In ETHZ-INS/epiwraps: epiwraps: Wrappers for plotting and dealing with epigenomics data

plotSignalTracks

Description

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"))
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")

ETHZ-INS/epiwraps documentation built on Dec. 22, 2024, 4:05 a.m.