beidsServer: Shiny module for searching BEIDs

In patzaw/BED: Biological Entity Dictionary (BED)

Shiny module for searching BEIDs

Description

Shiny module for searching BEIDs

Usage

beidsServer(
  id,
  toGene = TRUE,
  excludeTechID = FALSE,
  multiple = FALSE,
  beOfInt = NULL,
  selectBe = TRUE,
  orgOfInt = NULL,
  selectOrg = TRUE,
  searchLabel = "Search a gene",
  matchColname = "Match",
  oneColumn = FALSE,
  withId = FALSE,
  maxHits = 75,
  compact = FALSE,
  tableHeight = 150,
  highlightStyle = "",
  highlightClass = "bed-search"
)

beidsUI(id)

Arguments

id	an identifier for the module instance
toGene	focus on gene entities (default=TRUE): matches from other BE are converted to genes.
excludeTechID	do not display BED technical BEIDs
multiple	allow multiple selections (default=FALSE)
beOfInt	if toGene==FALSE, BE to consider (default=NULL ==> all)
selectBe	if toGene==FALSE, display an interface for selecting BE
orgOfInt	organism to consider (default=NULL ==> all)
selectOrg	display an interface for selecting organisms
searchLabel	display label for the search field or NULL for no label
matchColname	display name of the match column
oneColumn	if TRUE the hits are displayed in only one column
withId	if FALSE and one column, the BEIDs are not shown
maxHits	maximum number of raw hits to return
compact	compact display (default: FALSE)
tableHeight	height of the result table (default: 150)
highlightStyle	style to apply to the text to highlight
highlightClass	class to apply to the text to highlight

Value

A reactive data.frame with the following columns:

• beid: the BE identifier

• preferred: preferred identifier for the same BE in the same scope

• be: the type of biological entity

• source: the source of the identifier

• organism: the BE organism

• entity: internal identifier of the BE

• match: the matching character string

Functions

• beidsUI():

Examples

## Not run: 
library(shiny)
library(BED)
library(DT)

ui <- fluidPage(
   beidsUI("be"),
   fluidRow(
      column(
         12,
         tags$br(),
         h3("Selected gene entities"),
         DTOutput("result")
      )
   )
)

server <- function(input, output){
   found <- beidsServer("be", toGene=TRUE, multiple=TRUE, tableHeight=250)
   output$result <- renderDT({
      req(found())
      toRet <- found()
      datatable(toRet, rownames=FALSE)
   })
}

shinyApp(ui = ui, server = server)

## End(Not run)

patzaw/BED documentation built on Dec. 13, 2024, 4:29 a.m.