Generate the enrichment panel of the shiny app

These are the UI and server components of the enrichment panel of the shiny app. It is generated by including 'Enrichment' in the panels.default argument of generateShinyApp.

Usage

enrichmentPanelUI(id, show = TRUE)

enrichmentPanelServer(id, DEresults, organism, seed = 13)

Arguments

id

the input slot that will be used to access the value

show

whether to show the panel or not; default is TRUE; there for compatibility with specifying panels to show

DEresults

differential expression results output from DEpanelServer; a reactive list with slots 'DEtable' (all genes), 'DEtableSubset' (only DE genes), 'lfcThreshold' and 'pvalThreshold'

organism

organism name to be passed on to gprofiler2::gost; organism names are constructed by concatenating the first letter of the name and the family name; default is NA - enrichment is not included to ensure compatibility with datasets that have non-standard gene names; a vector (of the same length as modality) can be provided if length(modality) > 1

seed

the random seed to be set for the jitter plot, to avoid seemingly different plots for the same inputs

Value

The UI and Server components of the shiny module, that can be used within the UI and Server definitions of a shiny app.