Make an interactive gene set barcode plot with plotly — interactive

Reproduces the statistics drawn by barcodeplot (rank ordering, quantile shading and the enrichment "worm" curve) as an interactive plotly plot: rug ticks mark where gene set members fall in the statistic ranking, and a curve on a secondary axis shows local enrichment relative to the overall rate.

Usage

interactive_barcodeplot(
  fold_changes,
  gene_ids,
  set_gene_ids,
  labels = gene_ids,
  plot_title = "",
  worm_span = 0.45
)

Arguments

fold_changes: A numeric vector of fold changes (or other ranking statistic), one per gene
gene_ids: Gene IDs for the values in fold_changes, in the same ID space as set_gene_ids. Must be the same length and gene order as fold_changes and labels
set_gene_ids: Gene IDs for the gene set
labels: Display labels for the values in fold_changes, used in hover text (default: gene_ids). Must be the same length and gene order as fold_changes and gene_ids
plot_title: A title for the plot
worm_span: Span passed to the tricube moving average used for the enrichment curve (default: 0.45, matching limma's default)

Value

output A plotly plot object

Examples

set.seed(1)
gene_ids <- paste0("gene", 1:100)
fold_changes <- rnorm(100)
set_gene_ids <- sample(gene_ids, 15)
interactive_barcodeplot(fold_changes, gene_ids, set_gene_ids)