Quick standalone gene/region visualization from BigWig files

A zero-configuration entry point for visualizing any genomic locus with BigWig signal tracks. Requires only a gene symbol (or genomic coordinates) and one or more BigWig file paths. No database setup, no track connection CSV, no chromatin states — just signal overlaid on the gene model.

Usage

plot_quick_view(
  gene = NULL,
  region = NULL,
  bw_paths,
  labels = NULL,
  colors = NULL,
  genome = "hg38",
  txdb = NULL,
  organism = NULL,
  padding = 5000L,
  mirror = FALSE,
  signal_style = c("line", "polygon"),
  signal_layout = "auto",
  cex_cell_label = 1.4,
  cex_axis = 1.2,
  cex_coord = 1.3,
  cex_annotation = 1.1,
  cex_gene = 1.2,
  cex_title = 1.5,
  cex_signal_label = 1.2,
  quantile_cap = 0.98,
  scale_factor = 1.1,
  export = NULL,
  width = 10,
  height = 8
)

Arguments

gene: Character or NULL. HGNC gene symbol (e.g., "INS", "GCG"). Exactly one of gene or region must be provided.
region: List or NULL. Genomic coordinates as list(chr = "chr11", start = 2159779, end = 2161209). Exactly one of gene or region must be provided.
bw_paths: Named character vector of BigWig file paths. Names are used as sample labels. If names contain both "atac" and "rna" (case-insensitive), mirror pairing is attempted.
labels: Character vector or NULL. Override sample labels. If NULL, uses names(bw_paths).
colors: Character vector or NULL. Override sample colors. If NULL, uses a default colorblind-friendly palette. Must have the same length as bw_paths.
genome: Character. String name of the genome assembly associated with bw_paths (e.g. "hg38", "mm10", "rn6", "dm6"). The value must match the assembly recorded in the supplied txdb; a validator compares the string against GenomeInfoDb::genome(txdb). Defaults to "hg38" for convenience with built-in fallbacks.
txdb: Character or NULL. TxDb specification in "package::object" form (e.g. "TxDb.Rnorvegicus.UCSC.rn6.refGene:: TxDb.Rnorvegicus.UCSC.rn6.refGene"). If NULL, auto-resolved for the built-in convenience genomes "hg38" and "mm10"; for any other genome, txdb must be supplied explicitly.
organism: Character or NULL. org.db specification (e.g. "org.Rn.eg.db"). If NULL, auto-resolved for the built-in convenience genomes "hg38" and "mm10"; for any other genome, organism must be supplied explicitly.
padding: Integer. Base pairs of padding around gene/region (default 5000).
mirror: Logical. Enable mirrored ATAC/RNA layout (default FALSE).
signal_style: Character. Signal rendering style: "line" (default) draws vertical bars at each position (IGV/UCSC browser style), "polygon" draws filled area charts.
signal_layout: Character. Signal layout mode: "auto", "stacked", or "mirrored".
cex_cell_label: Numeric. Font size for cell type labels (default 1.4).
cex_axis: Numeric. Font size for axis labels (default 1.2).
cex_coord: Numeric. Font size for coordinate bar (default 1.3).
cex_annotation: Numeric. Font size for annotation labels (default 1.1).
cex_gene: Numeric. Font size for gene model labels (default 1.2).
cex_title: Numeric. Font size for plot title (default 1.5).
cex_signal_label: Numeric. Font size for signal indicators (default 1.2).
quantile_cap: numeric. Percentile for capping extreme signal peaks (default 0.98). Peaks above this percentile are clipped to prevent axis compression.
scale_factor: numeric. Y-axis headroom multiplier (default 1.1). Values above 1.0 add whitespace above the tallest signal peak.
export: Character or NULL. File path for export (pdf, eps, png, tiff).
width: Numeric. Export width in inches (default 10).
height: Numeric. Export height in inches (default 8).

Value

Invisible NULL. A multi-panel base-R plot is drawn on the current graphics device (or exported to file if export is set).

Details

This is the simplest way to use epiRomics for exploratory visualization. Specify a gene by symbol (e.g., "INS") or a region by coordinates. The function auto-resolves the TxDb annotation database for the specified genome assembly.

Examples

## plot_quick_view requires a TxDb (Suggests) and a real BigWig file.
## This example confirms that input validation fires correctly.
if (requireNamespace("TxDb.Hsapiens.UCSC.hg38.knownGene", quietly = TRUE)) {
  bw_path <- make_example_bigwig()
  tryCatch(
    plot_quick_view(
      region = list(chr = "chr1", start = 1000L, end = 51000L),
      bw_paths = c(Sample = bw_path),
      genome   = "hg38"
    ),
    error = function(e) message(e$message)
  )
  file.remove(bw_path)
}
#>   2169 genes were dropped because they have exons located on both strands of
#>   the same reference sequence or on more than one reference sequence, so cannot
#>   be represented by a single genomic range.
#>   Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
#>   object, or use suppressMessages() to suppress this message.

#> [1] TRUE