Help for package isoexplorer

Title:

GUI Components to Explore Stable Isotope Data Files

Version:

0.4.1

Description:

Provides graphical user interface components to explore stable isotope data files using the 'isoreader2' package, including browsing, visualizing, and exporting isotope data.

License:

AGPL (≥ 3)

Encoding:

UTF-8

Depends:

R (≥ 4.5.0)

Imports:

cli (≥ 3.6.0), rlang (≥ 1.1.0), tibble, dplyr, purrr, stringr, htmltools, shiny, bslib, shinyjs, shinyAce, shinycssloaders, rlog, DT, ggplot2, isoreader2 (≥ 0.6.0), stats, callr, httpuv, htmlwidgets, tidyr, tidyselect, tools, utils, withr

Suggests:

testthat (≥ 3.0.0), pkgload

Config/testthat/edition:

URL:

https://github.com/isoverse/isoexplorer

BugReports:

https://github.com/isoverse/isoexplorer/issues

Language:

en-US

Config/roxygen2/version:

8.0.0

NeedsCompilation:

Packaged:

2026-07-14 08:04:08 UTC; seko0922

Author:

Sebastian Kopf

[aut, cre]

Maintainer:

Sebastian Kopf <sebastian.kopf@colorado.edu>

Repository:

CRAN

Date/Publication:

2026-07-22 08:00:02 UTC

isoexplorer: GUI components to Explore Stable Isotope Data Files

Description

Provides graphical user interface components to explore stable isotope data files using the 'isoreader2' package, including browsing, visualizing, and exporting isotope data.

Author(s)

Maintainer: Sebastian Kopf sebastian.kopf@colorado.edu (ORCID)

Authors:

Sebastian Kopf sebastian.kopf@colorado.edu (ORCID)

Continuous flow plot module

Description

A plot view for continuous flow trace data, wired to a ie_file_server(): it plots the selection-filtered aggregated traces with isoreader2::ir_plot_continuous_flow(), with unit, species/mass, legend, zoom and PDF-download controls. Pair ie_cf_plot_ui() and ie_cf_plot_server() on one id.

Usage

ie_cf_plot_ui(id)

ie_cf_plot_server(id, file)

Arguments

id

the module id (must match the paired ie_metadata_ui())

file

the ie_file_server() handle

Value

ie_cf_plot_ui() returns a UI element; ie_cf_plot_server() returns a list with a get_code generator for the code server (see ie_code_server())

Examples

if (interactive()) {
  library(shiny)
  iso <-
    isoreader2::ir_examples_folder() |>
    isoreader2::ir_find_isofiles() |>
    isoreader2::ir_read_isofiles()

  ui <- ie_type_explorer_ui("meta", ie_cf_plot_ui("cf"))
  server <- function(input, output, session) {
    file <- ie_file_server("files", get_isofiles = reactive(iso))
    ie_cf_metadata_server("meta", file)
    ie_cf_plot_server("cf", file)
  }
  shinyApp(ui, server)
}

Code-generation server

Description

A central module that assembles "idealized example code" for an isoexplorer app and shows it in a viewer. It is instantiated once at the top level; every other module that can contribute code returns a get_code() generator, and the top-level wiring registers each one here with register() under an id, a heading, and (optionally) the id it depends_on.

Usage

ie_code_server(id, get_active_group = reactive(NULL))

ie_code_ui(id)

Arguments

id

the module id (namespace); pair with ie_code_ui() on the same id

get_active_group

a reactive returning the active group id; only registrations in this group (plus group-less ones) are shown. The default reactive(NULL) shows everything.

Details

The registrations form a dependency tree. When the user clicks the navbar Show code button (ie_code_ui()), the registered generators are walked depth-first and assembled into one document: the tree depth sets the heading level (⁠#⁠ for a root such as a read step, ⁠##⁠ for a step depending on a root, ⁠###⁠ for one depending on that, ...), and each step's output variable is threaded in as the input_var of the steps that depend on it. The document is shown in a read-only shinyAce::aceEditor() with a clickable headings tree (jump-to-section), a toggle between plain code and a Quarto view, and a .qmd download.

Each registration may carry a group; when get_active_group() returns a non-empty value only registrations in that group (plus group-less ones) are shown – the full multi-tab app uses this to show just the active measurement type's code.

Value

the code handle: a list with register(code_id, heading, get_code, depends_on = NULL, group = NULL) (each depends_on is a single id – the tree is single-parent) and build_document(quarto = FALSE) (assemble + return list(script, headings); exposed mainly for testing).

Functions

ie_code_ui(): the navbar Show code button (place in the navbar, e.g. bslib::nav_item(ie_code_ui("code"))) plus the one-time JS used to jump the editor to a heading. Pair with ie_code_server() on the same id.

The `get_code()` contract

a registered generator is ⁠function(input_var = NULL)⁠ returning ⁠list(code = <string>, output = <string or NULL>)⁠. It is called during assembly inside a reactive context, so it reflects the module's current state; input_var is the output variable of the module it depends on (NULL for a root), and output is the variable this snippet binds (or NULL for a terminal node such as a plot).

Examples

if (interactive()) {
  library(shiny)
  # ie_run_app() instantiates the code server for you; here it is wired
  # directly. Register each module's get_code generator into the dependency
  # tree; the "Show code" button (ie_code_ui()) assembles and displays it.
  ui <- bslib::page_fillable(ie_code_ui("code"))
  server <- function(input, output, session) {
    code <- ie_code_server("code")
    code$register("read", "Read data files", get_code = function(input_var = NULL) {
      list(
        code = 'iso <- ir_find_scans("data") |> ir_read_isofiles()',
        output = "iso"
      )
    })
    code$register("agg", "Aggregate data files", depends_on = "read",
      get_code = function(input_var = NULL) {
        list(
          code = sprintf("scans <- %s |> ir_aggregate_isofiles()", input_var),
          output = "scans"
        )
      })
  }
  shinyApp(ui, server)
}

Create an isofiles server app for the isoexplorer GUI

Description

Builds the full isoexplorer Shiny app – one navbar tab per measurement type (continuous flow / dual inlet / scans), each with a file-selector sidebar and plot – and returns it as a shiny::shinyApp() object to run or deploy. Unlike the focused ie_explore_continuous_flow() explorers, this app does NOT take an ir_isofiles object – data arrives at runtime via the navbar Upload button, any watched monitoring_folders, and/or the Load examples button (a "get started" prompt is shown until something is loaded). Loaded examples are selected automatically; uploaded files are selected only when the upload modal's "Select the uploaded files" box is checked.

Usage

ie_create_isofiles_server(
  timezone = Sys.timezone(),
  options = list(),
  uiPattern = "/",
  enableBookmarking = "url",
  default_theme = app_themes(),
  upload_folder = NULL,
  monitoring_folders = NULL,
  examples_folder = "examples",
  temporary_storage = FALSE,
  max_upload_size = NULL,
  log_level = "TRACE"
)

Arguments

timezone

the timezone to use for datetime display

options

Named options that should be passed to the runApp call (these can be any of the following: "port", "launch.browser", "host", "quiet", "display.mode" and "test.mode"). You can also specify width and height parameters which provide a hint to the embedding environment about the ideal height/width for the app.

uiPattern

A regular expression that will be applied to each GET request to determine whether the ui should be used to handle the request. Note that the entire request path must match the regular expression in order for the match to be considered successful.

enableBookmarking

Can be one of "url", "server", or "disable". The default value, NULL, will respect the setting from any previous calls to enableBookmarking(). See enableBookmarking() for more information on bookmarking your app.

default_theme

the default bslib Bootstrap 5 theme preset

upload_folder

upload directory for the navbar upload button; NULL (the default) means no upload button, a path enables it; see ie_file_server()

monitoring_folders

folders to watch for new isofiles, read and added automatically (NULL = off); see ie_file_server()

examples_folder

directory the "Load examples" navbar button copies the isoreader2 bundled example files into and loads; "examples" by default (NULL hides the button)

temporary_storage

if TRUE, the upload dialog notes that uploaded files are stored only for the duration of the session (informational; default FALSE)

max_upload_size

maximum per-file upload size in MB (sets the shiny.maxRequestSize option); NULL (the default) keeps Shiny's ~5 MB default. Raw isofiles are often larger, so raise this when allowing uploads.

log_level

how verbosely the app logs; see ie_run_app(). Defaults to "TRACE" (log everything) for this server app, unlike the focused explorers which default to "WARN".

Details

Because it returns the app object unrun, launch it yourself (print it, or wrap it in shiny::runApp()) or hand it to a deployment tool (e.g. shinyapps.io / ShinyProxy).

Value

a shiny::shinyApp() object (unrun)

Examples

if (interactive()) {
  # build the full multi-tab server app and run it; load data via the navbar
  # "Load examples" / "Upload" buttons at runtime
  ie_create_isofiles_server() |> shiny::runApp()

  # enable uploads (raise the per-file cap for large raw isofiles)
  app <- ie_create_isofiles_server(
    upload_folder = "uploads",
    max_upload_size = 200
  )
  shiny::runApp(app)
}

Dual inlet plot module

Description

A plot view for dual inlet cycle data, wired to a ie_file_server(): it plots the selection-filtered aggregated cycles with isoreader2::ir_plot_dual_inlet(), with unit, species/mass, legend, zoom and PDF-download controls. Pair ie_di_plot_ui() and ie_di_plot_server() on one id.

Usage

ie_di_plot_ui(id)

ie_di_plot_server(id, file)

Arguments

id

the module id (must match the paired ie_metadata_ui())

file

the ie_file_server() handle

Value

ie_di_plot_ui() returns a UI element; ie_di_plot_server() returns a list with a get_code generator for the code server (see ie_code_server())

Examples

if (interactive()) {
  library(shiny)
  iso <-
    isoreader2::ir_examples_folder() |>
    isoreader2::ir_find_isofiles() |>
    isoreader2::ir_read_isofiles()

  ui <- ie_type_explorer_ui("meta", ie_di_plot_ui("di"))
  server <- function(input, output, session) {
    file <- ie_file_server("files", get_isofiles = reactive(iso))
    ie_di_metadata_server("meta", file)
    ie_di_plot_server("di", file)
  }
  shinyApp(ui, server)
}

Explore an ir_isofiles object by measurement type

Description

Focused apps for exploring an already-read ir_isofiles object one measurement type at a time: ie_explore_continuous_flow() / ie_explore_dual_inlet() / ie_explore_scans() each show that type's file-selector sidebar + plot, and ie_explore_metadata() shows just the selector table. The generated example code (navbar Show code) refers to the object by its variable_name. These take a fixed object only – for upload / folder monitoring / load-examples use ie_create_isofiles_server().

Usage

ie_explore_continuous_flow(
  isofiles,
  timezone = Sys.timezone(),
  options = list(),
  uiPattern = "/",
  enableBookmarking = "url",
  default_theme = app_themes(),
  initial_selection = FALSE,
  variable_name = NULL,
  detached = TRUE,
  launch = TRUE,
  log_level = "WARN"
)

ie_explore_dual_inlet(
  isofiles,
  timezone = Sys.timezone(),
  options = list(),
  uiPattern = "/",
  enableBookmarking = "url",
  default_theme = app_themes(),
  initial_selection = FALSE,
  variable_name = NULL,
  detached = TRUE,
  launch = TRUE,
  log_level = "WARN"
)

ie_explore_scans(
  isofiles,
  timezone = Sys.timezone(),
  options = list(),
  uiPattern = "/",
  enableBookmarking = "url",
  default_theme = app_themes(),
  initial_selection = FALSE,
  variable_name = NULL,
  detached = TRUE,
  launch = TRUE,
  log_level = "WARN"
)

ie_explore_metadata(
  isofiles,
  timezone = Sys.timezone(),
  options = list(),
  uiPattern = "/",
  enableBookmarking = "url",
  default_theme = app_themes(),
  initial_selection = FALSE,
  variable_name = NULL,
  detached = TRUE,
  launch = TRUE,
  log_level = "WARN"
)

Arguments

isofiles

the ir_isofiles object to explore (required)

timezone

timezone for datetime display

options

uiPattern

enableBookmarking

default_theme

default bslib Bootstrap 5 theme preset

initial_selection

what is selected on load, as a dplyr::filter() expression on the aggregated metadata: FALSE (the default) selects nothing, TRUE selects everything, and any other expression (e.g. grepl("std", file_name)) selects the matching files/analyses. See ie_file_server(). In detached mode the expression is re-evaluated in the separate process, so it must be self-contained (it cannot reference variables from your session).

variable_name

the name used for the object in the generated example code. Defaults to the deparsed expression you passed (so my_iso |> ie_explore_scans() uses "my_iso"); set it explicitly to override.

detached

if TRUE, the app is launched in a separate R process (via callr::r_bg(), the app handed over in a temporary .rds) and opened in your default browser, leaving the calling session free; closing the browser tab stops the app and the process (which is also killed if the calling session exits). Default FALSE.

launch

only relevant when detached = FALSE: if TRUE (the default) the app is run in the current session (blocking) with shiny::runApp(); if FALSE the shiny::shinyApp() object is returned unrun (for server deployment or manual launching). Ignored when detached = TRUE (a detached app is always run).

log_level

how verbosely the app logs; see ie_run_app() for the available levels. Defaults to "WARN" for the focused explorers.

Details

By default the app runs detached in a separate R process (see detached), so the calling session is not blocked, and it refuses to launch while a document is being rendered (knitr / Quarto), showing a message to run it interactively. These are thin wrappers over ie_run_app(), which manages detached / launch.

Value

the value of ie_run_app() for the chosen detached / launch: the callr::r_bg() process (detached), the shiny::runApp() result (in-session launch), or the shiny::shinyApp() object (launch = FALSE).

Functions

ie_explore_dual_inlet(): focused app for the dual inlet plot.
ie_explore_scans(): focused app for the scans plot.
ie_explore_metadata(): focused app showing just the scans metadata selector table (handy for browsing/testing the selector).

Examples

if (interactive()) {
  # read the bundled isoreader2 examples (a mixed set of all types); each
  # explorer filters the object to its own measurement type
  iso <-
    isoreader2::ir_examples_folder() |>
    isoreader2::ir_find_isofiles() |>
    isoreader2::ir_read_isofiles()

  # each focused explorer opens the object in a detached browser app
  ie_explore_continuous_flow(iso)
  ie_explore_dual_inlet(iso)
  ie_explore_scans(iso)
  ie_explore_metadata(iso) # just the selector table

  # preselect some files and run blocking in the current session instead
  ie_explore_continuous_flow(
    iso,
    initial_selection = grepl("gc", file_name),
    detached = FALSE
  )
}

Central file-management module

Description

The single source of truth for the isofiles in an isoexplorer app, and the hub every other module talks to. It maintains a running set of read isofiles (seeded from get_isofiles(), grown by uploads and watched folders), splits it into the three measurement types (scans / continuous flow / dual inlet) with isoreader2::ir_filter_for_scans() and friends, owns the shared intensity-units selection and the per-type file selection, and exposes the per-type metadata (for the ie_metadata_server() selector tables) and the selection-filtered aggregated data (for the ⁠*_plot_server()⁠ modules).

Usage

ie_file_server(
  id,
  get_isofiles,
  initial_selection = TRUE,
  upload_folder = NULL,
  monitoring_folders = NULL,
  examples_folder = NULL,
  temporary_storage = FALSE
)

ie_file_ui(id)

Arguments

id

the module id (namespace)

get_isofiles

a reactive returning an ir_isofiles to seed the app with (already read); reactive(NULL) is fine when files only arrive via upload / monitoring

initial_selection

what is selected, per type, before any selector pushes a selection. An expression evaluated as a dplyr::filter() on the type's aggregated metadata tibble: TRUE (default) selects everything, FALSE selects nothing, and any other expression selects the matching rows (e.g. grepl("std", file_name)). Captured via tidy evaluation, so it may reference variables from the calling environment. Passed pre-quoted (a quosure) by the ⁠ie_explore_*()⁠ / ie_run_app() wrappers.

upload_folder

directory where uploaded files are stored (created on demand); NULL (the default) means no upload button – set a directory path to enable uploads.

monitoring_folders

character vector of folders to watch; isofiles found there with isoreader2::ir_find_isofiles() are read and added automatically. NULL (default) disables monitoring.

examples_folder

directory the "Load examples" navbar button copies the isoreader2 bundled example files into (and then loads). NULL (the default) means no examples button.

temporary_storage

if TRUE, the upload dialog states that uploaded files are stored only for the duration of the session. Informational only – it does not change how or where files are stored (default FALSE).

Details

Selector tables read ⁠get_<type>_metadata()⁠ and push their selection via ⁠set_selected_<type>()⁠; plot modules read ⁠get_aggregated_<type>_data()⁠ and drive the shared units via get_units() / set_units().

Dynamic files. New files (uploaded, or appearing in monitoring_folders) are read with isoreader2::ir_read_isofiles() and appended; aggregation is incremental (only new files are read/aggregated, then combined with c()), so already-read files are never re-read.

Upload. When upload_folder is set the module owns a navbar upload button (the ie_file_ui() placeholder) that opens a modal to upload multiple files or whole folders bundled as .zip archives (the picker allows .zip, the file types isoreader2 reads, and .json – which covers their ⁠.<type>.json⁠ serializations such as foo.cf.json). Uploaded files are stored in upload_folder (archives unpacked), and only the just-uploaded files are read – files already present in upload_folder when the app started are left untouched. An "Auto-select the newly uploaded files" checkbox (off by default) exclusively selects the new files in the relevant type's table and, in the full multi-tab app, switches to that type's tab.

Monitoring. monitoring_folders are polled; any isofiles found there with isoreader2::ir_find_isofiles() (including files already present at startup) are read and added.

Getting started. When examples_folder and/or upload_folder is set but the app is launched without data (empty get_isofiles()), a prompt is shown once inviting the user to load the examples and/or upload their own files; an app launched with data never sees it.

Value

The "file handle": a list of reactive accessors / setters. For each ⁠<type>⁠ in scans / cf / di: get_units()/set_units(units) (shared intensity units, default "mV"); ⁠get_<type>_metadata()⁠; ⁠set_selected_<type>(rows)⁠; ⁠get_<type>_selection()⁠; ⁠get_aggregated_<type>_data()⁠; plus ⁠get_<type>_select_signal()⁠ (file paths a selector should select, fired by upload auto-select) and get_active_type() (the type whose tab to activate after an auto-select).

Functions

ie_file_ui(): the navbar placeholders for the "Load examples" and "Upload" buttons (each rendered only when the server's examples_folder / upload_folder is set). Pair with ie_file_server() on the same id.

Examples

if (interactive()) {
  library(shiny)
  # read the bundled isoreader2 examples for some scans data
  iso <-
    isoreader2::ir_examples_folder() |>
    isoreader2::ir_find_isofiles() |>
    isoreader2::ir_read_isofiles()

  ui <- bslib::page_fillable(
    ie_type_explorer_ui("meta", ie_scans_plot_ui("scan"))
  )
  server <- function(input, output, session) {
    # the hub: every other module reads/writes through this handle
    file <- ie_file_server("files", get_isofiles = reactive(iso))
    ie_scans_metadata_server("meta", file) # selection -> file server
    ie_scans_plot_server("scan", file)     # file server -> plot
  }
  shinyApp(ui, server)
}

Metadata selector module

Description

Server for a file/analysis selector table (pair with ie_metadata_ui()). It shows a row-grouped table over an already-aggregated metadata tibble and pushes the current selection out via set_selected; double-clicking a row selects just that analysis, double-clicking a file's group header selects all of its analyses. Most users want the typed wrappers ie_scans_metadata_server() / ie_cf_metadata_server() / ie_di_metadata_server(), which bind the right ie_file_server() accessors; ie_metadata_server() itself is the generic version for wiring a custom metadata source.

Usage

ie_metadata_server(
  id,
  get_metadata,
  set_selected = NULL,
  get_selection = NULL,
  get_select_signal = NULL
)

Arguments

id

the module id (must match the paired ie_metadata_ui())

get_metadata

a reactive returning the metadata tibble to browse (one row per analysis, with uidx + analysis columns)

set_selected

optional ⁠function(rows)⁠ called with the selected metadata rows whenever the selection changes (e.g. file$set_selected_scans)

get_selection

optional reactive of the current selection, used to reflect it in the table on load (e.g. file$get_scans_selection)

get_select_signal

optional reactive carrying file paths the table should exclusively select (e.g. file$get_scans_select_signal, fired by upload auto-select); applied once the table contains those files

Value

a list with the underlying selector-table handle plus the get_selected_row_id / get_selected_metadata reactives

Examples

if (interactive()) {
  library(shiny)
  iso <-
    isoreader2::ir_examples_folder() |>
    isoreader2::ir_find_isofiles() |>
    isoreader2::ir_read_isofiles()

  ui <- ie_metadata_ui("meta")
  server <- function(input, output, session) {
    file <- ie_file_server("files", get_isofiles = reactive(iso))
    # the generic selector wired to any aggregated-metadata accessors; most
    # users want the typed wrappers ie_scans_metadata_server() / _cf_ / _di_
    ie_metadata_server(
      "meta",
      get_metadata = file$get_scans_metadata,
      set_selected = file$set_selected_scans,
      get_selection = file$get_scans_selection
    )
  }
  shinyApp(ui, server)
}

Metadata selector table UI

Description

The UI for a ie_metadata_server() file/analysis selector: a fullscreen-capable card with a toolbar (select-all / deselect on the left, column / search controls on the right) above a table that fills the rest of the card. Pair it with one of the ⁠*_metadata_server()⁠ functions using the same id.

Usage

ie_metadata_ui(id)

Arguments

id

the module id (must match the paired ⁠*_metadata_server()⁠)

Value

a bslib::card() UI element

Examples

# pair with a *_metadata_server() on the same id inside a shiny app
ie_metadata_ui("meta")

Assemble and launch a custom isoexplorer app

Description

Wraps your own module composition in the isoexplorer navbar shell (theme picker, dark-mode toggle, about popup) and, by default, runs it. Build your layout from the package's modules, instantiate the ie_file_server() and wire the modules in setup_modules. Supply EITHER main (a single content area) OR nav_panels (a centered navbar tabset).

Usage

ie_run_app(
  isofiles,
  main = NULL,
  setup_modules,
  timezone = Sys.timezone(),
  default_theme = app_themes(),
  nav_panels = NULL,
  selected = NULL,
  initial_selection = TRUE,
  upload_folder = NULL,
  monitoring_folders = NULL,
  examples_folder = NULL,
  temporary_storage = FALSE,
  max_upload_size = NULL,
  options = list(),
  uiPattern = "/",
  enableBookmarking = "url",
  detached = FALSE,
  launch = TRUE,
  stop_on_close = detached,
  log_level = c("WARN", "INFO", "DEBUG", "TRACE", "ERROR", "FATAL")
)

Arguments

isofiles

the ir_isofiles to explore (handed to the ie_file_server())

main

a single UI content area (use this OR nav_panels)

setup_modules

⁠function(file, code)⁠ that wires the app's server modules, given the ie_file_server() handle and the ie_code_server() handle (register each module's get_code with code$register()). A one-argument ⁠function(file)⁠ is still accepted (the code server is then not populated).

timezone

timezone for datetime display

default_theme

default bslib Bootstrap 5 theme preset

nav_panels

a list of bslib::nav_panel()s shown as a centered navbar tabset (use this OR main)

selected

the value/title of the nav_panels tab to open initially (NULL = the first tab)

initial_selection

initial file selection, see ie_file_server()

upload_folder

upload directory for the navbar upload button; NULL (the default) means no upload button, see ie_file_server()

monitoring_folders

folders to watch for new isofiles (NULL = off), see ie_file_server()

examples_folder

directory for the "Load examples" navbar button (NULL = off), see ie_file_server()

temporary_storage

note in the upload dialog that uploads are session-only (informational; default FALSE), see ie_file_server()

max_upload_size

maximum per-file upload size in MB; sets the shiny.maxRequestSize option for the running app. NULL (the default) leaves Shiny's ~5 MB default (or a value you set yourself) untouched. Raw isofiles are often larger than 5 MB, so raise this when enabling uploads.

options

uiPattern

enableBookmarking

detached

launch

stop_on_close

if TRUE, the app stops itself when the browser disconnects (session$onSessionEnded()); set automatically for the detached process so it exits when the tab is closed. Defaults to the same as detached.

log_level

how verbosely the app logs, one of "WARN" (the default – only warnings and errors), "INFO", "DEBUG", "TRACE" (everything), "ERROR", or "FATAL". Sets the LOG_LEVEL environment variable that rlog reads (also applied in the detached process).

Details

The detached / launch arguments control how it runs: detached = TRUE launches it in a separate R process (leaving this session free); ⁠detached = FALSE, launch = TRUE⁠ (the default) runs it in the current session (blocking) with shiny::runApp(); ⁠detached = FALSE, launch = FALSE⁠ returns the shiny::shinyApp() object unrun (for deployment or manual launching). The focused explorers (ie_explore_continuous_flow() etc.) and ie_create_isofiles_server() are wrappers that call this with the appropriate detached / launch.

Value

When detached = TRUE, the callr::r_bg() process (invisibly, with the app URL attached as an attribute); when detached = FALSE and launch = TRUE, the result of shiny::runApp() (after the app stops); when detached = FALSE and launch = FALSE, the shiny::shinyApp() object.

Examples

if (interactive()) {
  # read the bundled isoreader2 examples (a mixed set of all types)
  iso <-
    isoreader2::ir_examples_folder() |>
    isoreader2::ir_find_isofiles() |>
    isoreader2::ir_read_isofiles()

  # a minimal custom app: a scans selector next to a scans plot
  ie_run_app(
    isofiles = iso,
    main = ie_type_explorer_ui("meta", ie_scans_plot_ui("scan")),
    setup_modules = function(file, code) {
      ie_scans_metadata_server("meta", file)
      ie_scans_plot_server("scan", file)
    }
  )
}

Scans plot module

Description

A plot view for scan data, wired to a ie_file_server(): it plots the selection-filtered aggregated scans with isoreader2::ir_plot_scans(), with unit, species/mass, legend, zoom and PDF-download controls plus a scan-type popover (scans are plotted one type at a time). Pair ie_scans_plot_ui() and ie_scans_plot_server() on one id.

Usage

ie_scans_plot_ui(id)

ie_scans_plot_server(id, file)

Arguments

id

the module id (must match the paired ie_metadata_ui())

file

the ie_file_server() handle

Value

ie_scans_plot_ui() returns a UI element; ie_scans_plot_server() returns a list with a get_code generator for the code server (see ie_code_server())

Examples

if (interactive()) {
  library(shiny)
  iso <-
    isoreader2::ir_examples_folder() |>
    isoreader2::ir_find_isofiles() |>
    isoreader2::ir_read_isofiles()

  ui <- ie_type_explorer_ui("meta", ie_scans_plot_ui("scan"))
  server <- function(input, output, session) {
    file <- ie_file_server("files", get_isofiles = reactive(iso))
    ie_scans_metadata_server("meta", file)
    ie_scans_plot_server("scan", file) # reads the selection-filtered data
  }
  shinyApp(ui, server)
}

File-selector + plot layout for one measurement type

Description

Convenience UI combining a left file-selector sidebar (a ie_metadata_ui()) with a plot to its right – the building block each focused explorer and each tab of ie_create_isofiles_server() uses. Wire the matching ⁠*_metadata_server()⁠ (on meta_id) and ⁠*_plot_server()⁠ in your server function.

Usage

ie_type_explorer_ui(meta_id, plot_ui)

Arguments

meta_id

the id for the ie_metadata_ui() / ⁠*_metadata_server()⁠ pair

plot_ui

a plot module UI element, e.g. ie_scans_plot_ui("scan")

Value

a bslib::layout_sidebar() UI element

Examples

# a file-selector sidebar next to a scans plot (place inside a shiny UI)
ie_type_explorer_ui("meta", ie_scans_plot_ui("scan"))

Typed metadata selectors

Description

Selector-table servers wired to a ie_file_server() for one measurement type: they read that type's metadata and push the selection back into the file server. Pair each with a ie_metadata_ui() using the same id.

Usage

ie_scans_metadata_server(id, file)

ie_cf_metadata_server(id, file)

ie_di_metadata_server(id, file)

Arguments

id

the module id (must match the paired ie_metadata_ui())

file

the ie_file_server() handle

Value

a ie_metadata_server() handle

Examples

if (interactive()) {
  library(shiny)
  iso <-
    isoreader2::ir_examples_folder() |>
    isoreader2::ir_find_isofiles() |>
    isoreader2::ir_read_isofiles()

  ui <- ie_metadata_ui("meta")
  server <- function(input, output, session) {
    file <- ie_file_server("files", get_isofiles = reactive(iso))
    # pushes the table's selection into the file server for this type
    ie_scans_metadata_server("meta", file)
  }
  shinyApp(ui, server)
}

Package {isoexplorer}

isoexplorer: GUI components to Explore Stable Isotope Data Files

Description

Author(s)

See Also

Continuous flow plot module

Description

Usage

Arguments

Value

See Also

Examples

Code-generation server

Description

Usage

Arguments

Details

Value

Functions

The get_code() contract

Examples

Create an isofiles server app for the isoexplorer GUI

Description

Usage

Arguments

Details

Value

Examples

Dual inlet plot module

Description

Usage

Arguments

Value

See Also

Examples

Explore an ir_isofiles object by measurement type

Description

Usage

Arguments

Details

Value

Functions

Examples

Central file-management module

Description

Usage

Arguments

Details

Value

Functions

Examples

Metadata selector module

Description

Usage

Arguments

Value

Examples

Metadata selector table UI

Description

Usage

Arguments

Value

See Also

Examples

Assemble and launch a custom isoexplorer app

Description

Usage

Arguments

Details

Value

Examples

Scans plot module

Description

Usage

Arguments

Value

See Also

Examples

File-selector + plot layout for one measurement type

Description

The `get_code()` contract