Plot the transcripts involved in splicelogic events — plot

Draws one row per transcript appearing in tx_id or event_tx_id of events. Transcripts are coloured by the sign of their estimate (blue when positive, red when negative), and the exons called as events are filled by event type, outlined, and labelled with the type. An exon called as several types at once, e.g. an a5ss and an a3ss when both of its boundaries moved, is filled with the first type and striped diagonally with the others. A bent arrow over the first exon marks where each transcript starts and which way it runs.

Usage

plot_transcripts(
  events,
  exons,
  title = NULL,
  up_color = "#1f77b4",
  down_color = "#d62728",
  event_colors = event_palette(),
  unknown_color = "#999999",
  rescale_introns = TRUE,
  new_intron_length = 50,
  flanking_length = c(50, 50),
  transcript_label = TRUE,
  label_events = TRUE,
  label_size = 2.6,
  legend = TRUE,
  tx_annot = NULL,
  stripe_multi_events = TRUE
)

Arguments

events: A GRanges returned by find_all_events() or any find_*() function.
exons: A flat GRanges of exons with a tx_id column holding every transcript in events, e.g. the preprocessed GRanges the events were found in.
title: Plot title. Default NULL.
up_color, down_color: Colours for transcripts with a positive and a negative estimate.
event_colors: Named vector mapping event type to fill colour. Default event_palette().
unknown_color: Fill for event types absent from event_colors.
rescale_introns: Whether gaps between exons are shortened to new_intron_length. Default TRUE.
new_intron_length: Length (bp) of each gap after rescaling. Default 50.
flanking_length: Length (bp) of the region drawn before the first and after the last exon. Default c(50, 50).
transcript_label: Whether to print the transcript id and estimate above each row. Default TRUE.
label_events: Whether to print the event type below each event exon. Default TRUE.
label_size: Size of the event labels. Default 2.6.
legend: Whether to draw the fill legend. Default TRUE.
tx_annot: Optional character vector named by transcript id, appended to that transcript's label (e.g. novel status). Transcripts not named in it keep the plain label.
stripe_multi_events: Whether an exon called as several event types is striped with the types its fill leaves out. Default TRUE; FALSE fills it with the first type alone, and drops the others from the legend.

Value

A ggplot object.

Details

All events passed in are drawn on one panel, so they must come from a single gene; events from several genes are an error. Subset first, or use plot_transcripts_by_gene() for one plot per gene and plot_transcripts_by_pair() for one plot per transcript pair. A single event, e.g. plot_transcripts(events[1], exons), draws its two transcripts.

A per-transcript value such as a fold change is drawn separately by plot_transcript_lfc(). Given the same events, the two plots share their row order and y limits, so they line up side by side.

Examples

# one gene: "down" has three exons, "up" skips the middle one
exons <- data.frame(
  seqnames = "chr1",
  start = c(1, 201, 401, 1, 401),
  end = c(100, 300, 500, 100, 500),
  strand = "+",
  gene_id = "g1",
  tx_id = c("down", "down", "down", "up", "up"),
  exon_rank = c(1, 2, 3, 1, 2),
  estimate = c(-1, -1, -1, 1, 1)
) |>
  plyranges::as_granges() |>
  preprocess(coef_col = "estimate")

events <- find_all_events(exons, verbose = FALSE)

if (requireNamespace("ggplot2", quietly = TRUE)) {
  plot_transcripts(events, exons)
}