The locus panel drawn by Gviz

The same probes and the same gene model as dmsa_plot_locus, handed to Gviz instead of drawn here. Use this when you want what Gviz gives and this package does not: a real cytoband ideogram, transcript collapsing, and the ability to stack any other GdObject you already build - CpG islands, ATAC peaks, ChIP tracks, conservation - in the same coordinate frame.

Usage

dmsa_plot_locus_gviz(
  probes,
  gene = "",
  gene_model = NULL,
  chrom = NA,
  genome = "hg38",
  extra = list(),
  ideogram = FALSE,
  file = NULL,
  width = 1800,
  height = 1100,
  res = 190
)

Arguments

probes

Data frame with probe, pos, b, and optionally d, p, chr - the same frame dmsa_plot_locus() takes.

gene

Gene symbol, used for the title and the model lookup.

gene_model

A dmsa_gene_model, or TRUE to fetch one.

chrom

Chromosome, e.g. "chr5". Taken from the model or the probes when absent.

genome

Genome label passed to Gviz, default "hg38".

extra

A list of further Gviz tracks to stack under the model.

ideogram

Draw the cytoband ideogram. Needs network on first use, as Gviz fetches the band table from UCSC.

file

Optional PNG path.

width, height, res

PNG geometry.

Value

Invisibly, the list of tracks plotted.

Details

Gviz, GenomicRanges and IRanges are Suggests, not dependencies. This function errors with the install line if they are absent; everything else in the package keeps working without them.

See also

dmsa_plot_locus for the dependency-free panel.

Examples

if (FALSE) { # \dontrun{
gm <- dmsa_gene_model("NR3C1")
dmsa_plot_locus_gviz(pr, gene = "NR3C1", gene_model = gm)
} # }