GRNCisPanel: Generate the GRN cis integration panel of the shiny app

Description

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

Usage

GRNCisPanelUI(id, reference.table.name, comparison.table.name)
GRNCisPanelServer(
  id,
  expression.matrix,
  anno,
  coord.table.reference,
  coord.table.comparison,
  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
reference.table.name: Name for reference expression matrix and coordinate table
comparison.table.name: Name for comparison coordinate table
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
coord.table.reference: Table of coordinates corresponding to rows of expression.matrix
coord.table.comparison: Table of coordinates to compare against coord.table.reference
seed: Random seed to create reproducible GRNs