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 iflength(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
generateShinyAppusing the org.db specified