Generate the GRN custom integration panel of the shiny app

These are the UI and server components of the GRN custom integration panel of the shiny app. It is generated by including at least 1 row in the custom.integration parameter of generateShinyApp.

Usage

GRNCustomPanelUI(id, title = "GRN with custom integration", show = TRUE)

GRNCustomPanelServer(
  id,
  expression.matrix,
  anno,
  comparison.table,
  DEresults = NULL,
  seed = 13
)

Arguments

id

the input slot that will be used to access the value

title

Name for custom panel instance

show

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

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

comparison.table

Table linking rows of expression.matrix to custom information, for example miRNAs or transcription factors.

DEresults

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

seed

Random seed to create reproducible GRNs

Value

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