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
.
modalityPanelUI(id, metadata, organism, panels.default)modalityPanelServer(
id,
expression.matrix,
metadata,
anno,
organism,
panels.default
)
The UI and Server components of the shiny module, that can be used within the UI and Server definitions of a shiny app.
the input slot that will be used to access the value
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 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
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
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
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