modalityPanel {bulkAnalyseR}

Generate an app panel for a modality

Description

These are the UI and server components of a modality panel of the shiny app. Different modalities can be included by specifying their inputs in generateShinyApp.

Usage

modalityPanelUI(id, metadata, organism, panels.default)

modalityPanelServer(
  id,
  expression.matrix,
  metadata,
  anno,
  organism,
  panels.default
)

Arguments

id

the input slot that will be used to access the value

metadata

a data frame containing metadata for the samples contained in the expression.matrix; must contain at minimum two columns: the first column must contain the column names of the expression.matrix, while the last column is assumed to contain the experimental conditions that will be tested for differential expression; a list (of the same length as modality) can be provided if #' length(modality) > 1

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

panels.default

argument to control which of the default panels will be included in the app; default is all, but the enrichment panel will not appear unless organism is also supplied; note that the 'DE' panel is required for 'DEplot', 'DEsummary', 'Enrichment', and 'GRNenrichment'; a list (of the same length as modality) can be provided if length(modality) > 1

expression.matrix

the expression matrix; rows correspond to genes and columns correspond to samples; usually preprocessed by preprocessExpressionMatrix; a list (of the same length as modality) can be provided if #' length(modality) > 1

anno

annotation data frame containing a match between the row names of the expression.matrix (usually ENSEMBL IDs) and the gene names that should be rendered within the app and in output files; this object is created by generateShinyApp using the org.db specified

Value

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