Shiny module for searching BEIDs
Usage
beidsServer(
id,
toGene = TRUE,
excludeTechID = FALSE,
multiple = FALSE,
beOfInt = NULL,
selectBe = TRUE,
orgOfInt = NULL,
selectOrg = TRUE,
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
- 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
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)
} # }