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

Source: R/plot_events.R
plot_transcripts_by_gene.Rd

Splits events by gene_id and draws each gene with plot_transcripts().

Usage

plot_transcripts_by_gene(events, exons, genes = NULL, title = NULL, ...)

Arguments

events

A GRanges returned by find_all_events() or any find_*() function, with a gene_id column.

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.

genes

Optional character vector of gene ids to restrict to.

title

Optional prefix for the plot titles, which are otherwise the gene id.

...

Passed to plot_transcripts().

Value

A named list of ggplot objects, one per gene.

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_gene(events, exons)
  plots[["g1"]]
}