Plot isoforms

Plot isoforms, either from a gene or a list of transcript ids.

Usage

plot_isoforms(
  sce,
  gene_id,
  transcript_ids,
  n = 4,
  format = "plot_grid",
  colors
)

Arguments

sce

The SingleCellExperiment object containing transcript counts, rowRanges and rowData with gene_id and transcript_id columns.

gene_id

The gene symbol of interest, ignored if transcript_ids is provided.

transcript_ids

The transcript ids to plot.

n

The number of top isoforms to plot from the gene. Ignored if transcript_ids is provided.

format

The format of the output, either "plot_grid" or "list".

colors

A character vector of colors to use for the isoforms. If not provided, gray will be used. for all isoforms.

Value

When format = "list", a list of ggplot objects is returned. Otherwise, a grid of the plots is returned.

Details

This function takes a SingleCellExperiment object and plots the top isoforms of a gene, or a list of specified transcript ids. Either as a list of plots or together in a grid. This function wraps the ggbio::geom_alignment function to plot the isoforms, and orders the isoforms by expression levels (when specifying a gene) or by the order of the transcript_ids.

Examples

plot_isoforms(scmixology_lib10_transcripts, gene_id = "ENSG00000108107")
#> Constructing graphics...
#> Constructing graphics...
#> Constructing graphics...
#> Constructing graphics...