plot_exclusive_junctions: Plot transcript-exclusive splice junctions

In splikit: Analysing RNA Splicing in Single-Cell RNA Sequencing Data

Plot transcript-exclusive splice junctions

Description

Draws a gene-model view of a gene's transcripts (one row per transcript) with splice junctions rendered as arcs above each row. Junctions used by a single transcript of the gene ("transcript-exclusive") are drawn as solid black arcs; shared junctions as thin grey arcs. Works with both Ensembl-style and RefSeq-style GTFs: if a row has no gene_name attribute, gene_id is used; if no transcript_name, transcript_id is used.

Usage

plot_exclusive_junctions(
  gtf,
  target_gene,
  show_exclusive = TRUE,
  transcript = NULL,
  curvature = -0.2,
  out_file = NULL
)

Arguments

gtf	Either a path to an Ensembl- or RefSeq-style GTF, or a pre-loaded data.table of GTF rows.
target_gene	Gene symbol (matches gene_name, or gene_id if no gene_name is present).
show_exclusive	Logical (default TRUE). Restrict to transcripts that own >= 1 exclusive junction.
transcript	Optional character vector of transcript names to pin the plot to (overrides show_exclusive).
curvature	Numeric, arc-height knob for ggplot2::geom_curve().
out_file	Optional character. If given, the plot is also written to this file with ggplot2::ggsave().

Value

An S3 object of class "splikit_junction_plot" (a list) with components:

plot

A ggplot object.

info

A data.table with one row per drawn (transcript, junction) pair and columns gene_name, gene_id, transcript_name, transcript_id, chr, strand, j_start, j_end, j_width, exclusive, n_tx_with_junction, observed_in_eventdata, row_names_mtx, is_annot. For GTF-only calls the last three are NA.

exons, junctions, tx_order

The underlying tables used to build the plot, retained for advanced users.

Printing the object renders the plot and then prints info.

Required packages

Requires the ggplot2 package (declared in Suggests).

Examples

if (requireNamespace("ggplot2", quietly = TRUE)) {
  # Build a tiny synthetic GTF as a data.table (no external file needed).
  # tx1 has 3 exons (2 junctions); tx2 has 2 exons (1 junction).
  gtf <- data.table::data.table(
    seqname = "chr1",
    source  = "toy",
    type    = rep("exon", 5),
    start   = c(100, 300, 500, 100, 500),
    end     = c(200, 400, 600, 200, 600),
    score   = ".",
    strand  = "+",
    frame   = ".",
    attr    = c(
      'gene_name "FOO"; transcript_id "tx1"; exon_number "1";',
      'gene_name "FOO"; transcript_id "tx1"; exon_number "2";',
      'gene_name "FOO"; transcript_id "tx1"; exon_number "3";',
      'gene_name "FOO"; transcript_id "tx2"; exon_number "1";',
      'gene_name "FOO"; transcript_id "tx2"; exon_number "2";'
    )
  )
  res <- plot_exclusive_junctions(gtf, "FOO")
  res$info
}

splikit documentation built on May 13, 2026, 9:08 a.m.