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bulkAnalyseR (version 1.1.0)

modalityPanel: 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 )

Value

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

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