Plot the Genomic Context of a Gene's Isoforms — plot_genomic

Draws the exon-intron structure of every annotated transcript of one or more genes along the genome, one row per transcript, coloured by transcript type, with introns as lines carrying strand arrows. This is a pure ggplot2 implementation reading the exon table of the annotation directory, so it needs no genome packages. The IsoformicExperiment method can annotate each transcript with its mean expression and highlight differentially expressed isoforms.

The data frame method takes an exon table as returned by exon_table() or prepare_exon_annotation() (columns transcript_id, start_pos, end_pos, and optionally transcript_name, transcript_type, gene_name, seqid, strand). plot_tx_context() is kept as an alias of that method accepting the legacy column names tx_id, exon_left and exon_right.

Usage

plot_genomic_context(
  self,
  gene_name = NULL,
  assay = "abundance",
  highlight_de = TRUE,
  color_palette = NULL,
  expression = NULL,
  highlight = NULL,
  highlight_poison_exons = TRUE,
  upstream_offset = 0,
  downstream_offset = 0,
  exon_height = 0.6,
  ncol = 1L,
  ...
)

plot_tx_context(exon_table, ...)

Arguments

self: An IsoformicExperiment or an exon table.
gene_name: Character vector of gene names or IDs.
assay: Name of the assay used to label transcripts with their mean expression; NULL disables the labels.
highlight_de: Logical, outline isoforms flagged as significant in the stored transcript-level results.
color_palette: Named colour vector per transcript type; defaults to the object's palette or tx_type_palette().
expression: Optional named numeric vector (by transcript ID) used to label transcripts (data frame method).
highlight: Optional character vector of transcript IDs or names to outline (data frame method).
highlight_poison_exons: Logical, outline exons found only in unproductive isoforms of the gene (see poison_exons()).
upstream_offset, downstream_offset: Extra genomic span (bp) shown before and after the gene.
exon_height: Height of exon boxes (0-1).
ncol: Number of facet columns when several genes are plotted.
...: Passed on to methods.
exon_table: Legacy argument of plot_tx_context().

Value

A ggplot object.

Examples

iso <- example_isoformic()
plot_genomic_context(iso, gene_name = "RBPJ")
#> Warning: ! 1 transcript has a sequence length differing from the exon length; its ORF is
#>   skipped.

plot_genomic_context(iso, gene_name = "EGFR", assay = NULL, highlight_de = FALSE)


# Table-based
plot_genomic_context(exon_table(iso, "PNCK"))