GRNCustomPanel: Generate the GRN custom integration panel of the shiny app

Description

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
)

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
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