geneSetSelect: Create a selectize input to select a gene set from a sparrow...

In lianos/sparrow.shiny: Provides shiny modules to visualize sparrow results

Create a selectize input to select a gene set from a sparrow result.

Description

Take a look at the [reactiveGeneSetSelect()] module to select gene sets but also enable the user to first filter the genesets to choose from based on some global criteria.

Usage

geneSetSelect(
  input,
  output,
  session,
  src,
  server = TRUE,
  maxOptions = Inf,
  sep = "_::_"
)

geneSetSelectUI(id, label = "Select Gene Set")

updateGeneSetSelect(
  session,
  id,
  label = NULL,
  choices = NULL,
  selected = NULL,
  options = list(),
  server = FALSE
)

gs.render.select.ui(
  ns,
  choices,
  server = TRUE,
  maxOptions = 1000,
  sep = "_::_"
)

gs.select.choices(mg, sep = "_::_")

Arguments

input, output, session	the shiny-required bits for the module
src	A [SparrowResultContainer()] object
server	logical indicating wether the options should be generated in the server module, default: 'TRUE'
maxOptions	a paremeter used to customize the 'GeneSetSelect::selectizeInput' UI element to configure the maximum number of elements to include in the select dropdown, the remainder of the genesets will be loaded from the server side. Default: 'Inf' for all.
sep	the string used to concatenate geneset 'collection' and 'name' to generate a uniqe string for a geneset
id	the 'naked' module id
label	the label for the [shiny::selectizeInput()]
choices	the output of 'gs.select.choices(SparrowResult)'
selected	The initially selected value (or multiple values if multiple = TRUE). If not specified then defaults to the first value for single-select lists and no values for multiple select lists.
options	A list of options. See the documentation of selectize.js for possible options (character option values inside base::I() will be treated as literal JavaScript code; see renderDataTable() for details).
ns	the namespace function for this module
mg	'SparrowResult' to build options for

Details

This code was inspired from the dynamicSelectShinyModule.R gist.

Value

a reactive list of information about the selected geneset.

collection

the collection its from

name

the name within the collection

stats

a data.frame of "contrast statistics" for the features in the geneset

select.id

the shiny id for this module

sep

the separator used to key the collection,name string for this geneset

a properly wired '[shiny::selectizeInput()]' UI element.

'data.table' to populate 'choices' of 'selectizeInput'

Functions

• geneSetSelectUI: the ui for the module

• updateGeneSetSelect: update geneSetSelect externally. with new choices

• gs.render.select.ui: Internal function to build a 'selectizeInput' widget that is specific to a SparrowResult.

• gs.select.choices: Internal function to build a 'data.frame' used to populate geneset choices for a select input.

  Note that when returning a data.frame for the choices from 'gs.select.choice()', we need a column called '"value"' and a column called '"label"'.

  * 'value': the value that is sent back when an item is selected * 'label': athe text that appears in the selection after its triggered

Module Return

Returns information about the 'geneSetSelect' object

Examples

sres <- sparrow::exampleSparrowResult()
app <- shiny::shinyApp(
  ui = shiny::shinyUI(shiny::fluidPage(
    exampleUISetup(),
    title = "Gene Set Select",
    geneSetSelectUI("mod"))),
  server = function(input, output, session) {
    src <- shiny::reactive(SparrowResultContainer(sres))
    shiny::callModule(geneSetSelect, "mod", src)
  })
if (interactive()) {
  shiny::runApp(app)
}

lianos/sparrow.shiny documentation built on Oct. 12, 2023, 2:43 a.m.