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The server function of the genesetbarcodeplot module

Source: R/genesetbarcodeplot.R
genesetbarcodeplot.Rd

This module leverages gene sets stored in the gene_sets slot of an ExploratorySummarizedExperimentList object to produce interactive barcode plots, reproducing the statistics behind Limma's barcodeplot function. Genes are ranked by fold changes calculated with the contrasts module, and FDR values from the gene_set_analyses slot of the selected ExploratorySummarizedExperiment are displayed where provided.

Usage

genesetbarcodeplot(id, eselist)

Arguments

id

Module namespace

eselist

ExploratorySummarizedExperimentList object containing ExploratorySummarizedExperiment objects

Details

This function is called directly, using the same id as its UI counterpart, and wraps its logic in moduleServer() (see example).

Examples

if (interactive()) {
  data(airway, package = "airway")
  ese <- as(airway, "ExploratorySummarizedExperiment")
  eselist <- ExploratorySummarizedExperimentList(ese)
  genesetbarcodeplot("genesetbarcodeplot", eselist)

  # Almost certainly used via application creation

  app <- prepare_app("genesetbarcodeplot", eselist)
  shiny::shinyApp(ui = app$ui, server = app$server)
}