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Plot the transcripts involved in splicelogic events, one plot per pair

Source: R/plot_events.R
plot_transcripts_by_pair.Rd

Splits events by transcript pair, so each plot shows two transcripts and every event between them. The pair is unordered, so events reported from either side land in the same plot.

Usage

plot_transcripts_by_pair(events, exons, title = NULL, ...)

Arguments

events

A GRanges returned by find_all_events() or any find_*() function. A tx_pair column, if present, is used as the grouping as is.

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

Optional prefix for the plot titles, which are otherwise the transcript pair.

...

Passed to plot_transcripts().

Value

A named list of ggplot objects, one per transcript pair.

Examples

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)) {
  plots <- plot_transcripts_by_pair(events, exons)
  plots[["down-up"]]
}