Plot a per-transcript fold change for the transcripts of splicelogic events

Draws one diverging bar per transcript appearing in tx_id or event_tx_id of events: left of zero for a negative value and right for a positive one. It is the companion to plot_transcripts(): given the same events the two plots share their row order and y limits, so they line up when placed side by side, e.g. with patchwork.

Usage

plot_transcript_lfc(
  events,
  tx_lfc,
  title = NULL,
  lfc_max = NULL,
  lfc_label = "log2 fold change",
  lfc_ends = NULL,
  bar_color = "grey30",
  transcript_label = FALSE
)

Arguments

events

A GRanges returned by find_all_events() or any find_*() function.

tx_lfc

Numeric vector named by transcript id, e.g. a log2 fold change from a differential expression analysis. Transcripts not named in it keep their row but get no bar.

title

Plot title. Default NULL.

lfc_max

Half-width of the x axis. NULL (default) uses the largest absolute value in the plot; pass a number to make plots comparable. Values beyond it are clipped at the axis edge.

lfc_label

x-axis title.

lfc_ends

Optional length-2 character vector naming the negative and positive ends of the axis, e.g. c("KD", "WT") for a log2(WT/KD). Default NULL draws no end labels.

bar_color

Colour of the bars. Default "grey30".

transcript_label

Whether to print the transcript ids on the y axis, for use on its own. Default FALSE, as plot_transcripts() already labels the rows.

Value

A ggplot object.

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)
tx_lfc <- c(down = -1.8, up = 0.6)

if (requireNamespace("ggplot2", quietly = TRUE)) {
  plot_transcript_lfc(events, tx_lfc, transcript_label = TRUE)
}