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Shiny module for searching BEIDs

Source: R/beidsModule.R
beidsServer.Rd

Shiny module for searching BEIDs

Usage

beidsServer(
  id,
  toGene = TRUE,
  excludeTechID = FALSE,
  multiple = FALSE,
  beOfInt = NULL,
  selectBe = TRUE,
  orgOfInt = NULL,
  selectOrg = TRUE,
  groupBySymbol = FALSE,
  searchLabel = "Search a gene",
  matchColname = "Match",
  selectFirst = FALSE,
  oneColumn = FALSE,
  withId = FALSE,
  maxHits = 75,
  clean_id_search = TRUE,
  clean_name_search = TRUE,
  fuzzy = TRUE,
  compact = FALSE,
  tableHeight = 150,
  highlightStyle = "",
  highlightClass = "bed-search",
  inputUpdateOn = c("change", "blur")
)

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

groupBySymbol

if TRUE also use gene symbols to aggregate results with more granularity (taken into account only when toGene == TRUE)

searchLabel

display label for the search field or NULL for no label

matchColname

display name of the match column

selectFirst

if TRUE the first row is selected by default

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

clean x to avoid error during ID search. Default: TRUE. Set it to false if you're sure of your lucene query.

clean x to avoid error during ID search. Default: TRUE. Set it to false if you're sure of your lucene query.

fuzzy

if TRUE (default) a fuzzy search is applied on names and symbols.

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

inputUpdateOn

A character vector specifying when the input should be updated. Options are "change" (default) and "blur". Use "change" to update the input immediately whenever the value changes. Use "blur"to delay the input update until the input loses focus (the user moves away from the input), or when Enter is pressed.

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

if (FALSE) { # \dontrun{
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)
} # }