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Update to version 4.14.1
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‎.Rbuildignore‎

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^.*\.Rproj$
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^\.Rproj\.user$
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^doc$
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^Meta$
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^_pkgdown\.yml$
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^docs$
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^pkgdown$
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^sandbox$
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^script_pkgdown.R$
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^data-raw$
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dev_history.R
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^dev$
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$run_dev.*
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^LICENSE\.md$
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^README\.Rmd$
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^app\.R$
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^rsconnect$

‎DESCRIPTION‎

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Package: pr2database
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Type: Package
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Title: PR2 database
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Version: 4.14.0
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Author: Daniel Vaulot
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Maintainer: Daniel Vaulot <[email protected]>
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Title: PR2 database with shiny web interface
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Version: 4.14.1
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Authors@R: person('Daniel', 'Vaulot', email = '[email protected]', role = c('cre', 'aut'))
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Description: PR2 database
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See https://pr2-database.org
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License: CC-BY 4.0
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License: MIT + file LICENSE
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Imports:
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Biostrings,
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blaster (>= 1.0.4),
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config (>= 0.3.1),
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dplyr,
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DT,
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forcats,
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ggplot2,
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golem (>= 0.3.5),
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markdown,
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pkgload,
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purrr,
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qs,
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rio,
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shiny (>= 1.7.2),
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shinycssloaders,
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shinydisconnect,
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shinylogs,
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shinyvalidate,
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shinyWidgets,
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stringr,
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tidyr,
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yaml
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 7.1.2
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URL: https://github.com/pr2database
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BugReports: https://github.com/pr2database/issues
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Suggests:
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knitr,
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rmarkdown
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VignetteBuilder: knitr
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spelling,
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testthat (>= 3.0.0)
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Config/testthat/edition: 3
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Language: en-US
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Depends:
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R (>= 2.10)
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Remotes:
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manutamminen/blaster

‎NAMESPACE‎

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# Generated by roxygen2: do not edit by hand
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export(pr2_database)
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export(run_app)
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import(dplyr)
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import(forcats)
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import(ggplot2)
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import(markdown)
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import(shiny)
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import(stringr)
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importFrom(golem,activate_js)
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importFrom(golem,add_resource_path)
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importFrom(golem,bundle_resources)
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importFrom(golem,favicon)
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importFrom(golem,with_golem_options)
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importFrom(shiny,HTML)
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importFrom(shiny,column)
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importFrom(shiny,shinyApp)
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importFrom(shiny,tagAppendAttributes)
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importFrom(shiny,tagList)
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importFrom(shiny,tags)

‎R/app_config.R‎

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#' Access files in the current app
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#'
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#' NOTE: If you manually change your package name in the DESCRIPTION,
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#' don't forget to change it here too, and in the config file.
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#' For a safer name change mechanism, use the `golem::set_golem_name()` function.
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#'
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#' @param ... character vectors, specifying subdirectory and file(s)
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#' within your package. The default, none, returns the root of the app.
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#'
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#' @noRd
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app_sys <- function(...) {
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system.file(..., package = "pr2database")
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}
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#' Read App Config
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#'
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#' @param value Value to retrieve from the config file.
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#' @param config GOLEM_CONFIG_ACTIVE value. If unset, R_CONFIG_ACTIVE.
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#' If unset, "default".
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#' @param use_parent Logical, scan the parent directory for config file.
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#' @param file Location of the config file
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#'
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#' @noRd
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get_golem_config <- function(
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value,
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config = Sys.getenv(
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"GOLEM_CONFIG_ACTIVE",
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Sys.getenv(
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"R_CONFIG_ACTIVE",
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"default"
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)
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),
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use_parent = TRUE,
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# Modify this if your config file is somewhere else
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file = app_sys("golem-config.yml")
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) {
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config::get(
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value = value,
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config = config,
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file = file,
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use_parent = use_parent
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)
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}

‎R/app_server.R‎

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#' The application server-side
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#'
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#' @param input,output,session Internal parameters for {shiny}.
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#' DO NOT REMOVE.
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#' @import shiny
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#' @noRd
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app_server <- function(input, output, session) {
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# Your application server logic
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# Stop the application of the session is closed (after 30 min) - ACTIVATE for web application
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session$onSessionEnded(stopApp)
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# Disconnection
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observeEvent(input$button_disconnect, {session$close()})
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# To track usage
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shinylogs::track_usage(storage_mode = shinylogs::store_sqlite(path = "logs/"))
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# Taxonomy selection on left menu
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taxo_selected <- mod_select_taxonomy_server("select_taxonomy")
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# Separate sequences filtration from display so can be used in different panels
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sequences_filtered <- mod_filter_sequences_server("filter_sequences", taxo_selected)
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mod_table_taxonomy_server("table_taxonomy", pr2$taxonomy, taxo_selected)
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# Display table of sequences... It is necessary to pass taxo_selected to display correctly number of sequences
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mod_table_sequences_server("table_sequences", sequences_filtered, taxo_selected)
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# Download the data full and selected sequences
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mod_download_server("download", sequences_filtered, taxo_selected)
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# Query all sequences
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mod_query_server("query")
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}

‎R/app_ui.R‎

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#' The application User-Interface
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#'
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#' @param request Internal parameter for `{shiny}`.
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#' DO NOT REMOVE.
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#' @import shiny
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#' @noRd
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app_ui <- function(request) {
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tagList(
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# Leave this function for adding external resources
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golem_add_external_resources(),
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# Your application UI logic
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# --- Page with side bar layout
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fluidPage(
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# Message for disconnection
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shinydisconnect::disconnectMessage(
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text = "Server lost connection.",
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refresh = "Reload now"
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),
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title = "PR2 reference database",
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sidebarLayout(sidebar(),
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mainpanel()
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)
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)
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)
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}
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#' Add external Resources to the Application
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#'
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#' This function is internally used to add external
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#' resources inside the Shiny application.
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#'
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#' @import shiny
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#' @importFrom golem add_resource_path activate_js favicon bundle_resources
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#' @noRd
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golem_add_external_resources <- function() {
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add_resource_path(
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"www",
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app_sys("app/www")
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)
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add_resource_path(
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"readme",
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app_sys("app/readme")
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)
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add_resource_path(
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"data-qs",
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app_sys("app/data-qs")
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)
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tags$head(
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favicon(),
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bundle_resources(
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path = app_sys("app/www"),
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app_title = "PR2 database"
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),
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# Script to close the windows after some inactivity - ACTIVATE for web application
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tags$script(inactivity),
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)
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}

‎R/fct_select_taxonomy.R‎

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options_picker_taxo <- shinyWidgets::pickerOptions(
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actionsBox = TRUE,
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selectedTextFormat = "count > 3",
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liveSearch = TRUE,
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noneSelectedText = "All",
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showTick = TRUE,
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size = 5
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)
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options_picker_taxo_kingdom <- shinyWidgets::pickerOptions(
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actionsBox = TRUE,
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selectedTextFormat = "count > 3",
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liveSearch = TRUE,
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noneSelectedText = "None",
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showTick = TRUE,
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size = 5
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)
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# =================================
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# Small function to return the taxo level number
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#
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# @param taxo_level character
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#
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# @return the taxo_level number
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#
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# @noRd
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#
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# @examples taxo_level_number("genus")
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# # [1] 7
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#
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#
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taxo_level_number <- function(taxo_level) {
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which(global$taxo_levels == taxo_level)
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}
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#
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# =================================
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# Small function to return the taxo level and taxon name
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#
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# @param kingdom
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# @param supergroup
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# @param division
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# @param class
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# @param order
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# @param family
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# @param genus
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# @param species
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#
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# @return A named vector with 3 elements. The first level which is not NULL, the corresponding name or names and the taxo as a list
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#
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# @noRd
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# #
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# @examples
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#
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# taxo_return("Eukaryota","S", "D", "C", "O", c("F", "F1"), NULL, NULL)
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# # $level
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# # [1] "family"
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# #
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# # $name
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# # [1] "F" "F1"
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# #
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# # $kingdom
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# # [1] "Eukaryota"
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# #
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# # $supergroup
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# # [1] "S"
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# #
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# # $division
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# # [1] "D"
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# #
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# # $class
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# # [1] "C"
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# #
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# # $order
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# # [1] "O"
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# #
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# # $family
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# # [1] "F" "F1"
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# #
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# # $genus
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# # NULL
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# #
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# # $species
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# # NULL
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taxo_return <- function(kingdom, supergroup, division, class, order, family, genus, species) {
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taxo_1 <- c(kingdom[1], supergroup[1], division[1], class[1], order[1], family[1], genus[1], species[1])
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taxo_list <- list(kingdom = kingdom, supergroup = supergroup, division=division,
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class=class, order = order, family = family, genus = genus, species = species)
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# The levels for which nothing is selected return NULL and the length of the vector gives the first rank which is NULL
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if (length(taxo_1) == 0) {
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return( c(level = "kingdom", list(name = unique(global$kingdom)), taxo_list))
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}
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taxo_level <- global$taxo_levels[length(taxo_1)]
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message("Taxo level: ", taxo_level)
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# Then the name(s) are just extracted from the list for the taxo_level
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taxo_name <- taxo_list[[taxo_level]]
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message("Taxo name: ", taxo_name)
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# Very strange, the if one puts the name in the list then if there are more than one it is returned as several names (name1, name2 etc...)
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# See: https://stackoverflow.com/questions/9031819/add-named-vector-to-a-list
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return( c(level = taxo_level, list(name = taxo_name), taxo_list))
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}
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