Package 'ugplot'

ugplot: exploratory plots and model screening

Description

The ugplot package provides an interactive Shiny application to inspect data, create visual summaries, and evaluate predictive models.

---

Launch the ugplot Shiny application

Description

Starts the ugplot Shiny interface used to explore data relationships with heatmaps, 2D plots and predictive modeling workflows.

Usage

ugPlot(dataset = data.frame())

Arguments

dataset

A data frame to pre-load in the app. If empty, the app starts without a dataset.

Value

A shiny.appobj that runs the ugplot interface.

Examples

if (interactive()) {
  ugPlot()
}

---

Check caret model dependencies used by ugPlot

Description

Lists caret models whose required R packages are not installed in the current R library.

Usage

ugPlotCheckModelDeps(models = NULL, exclude_models = character())

Arguments

models	Optional character vector of caret model names. Defaults to all caret models.
exclude_models	Optional character vector of caret model names to skip.

Value

Invisibly returns dependency status tables and package names.

---

Install caret model dependencies used by ugPlot

Description

Installs the R packages required by missing caret models in the current R library. Run this on the machine that will execute the jobs, including the ugPlot server host.

Usage

ugPlotInstallModelDeps(
  models = NULL,
  install = TRUE,
  dependencies = TRUE,
  exclude_models = character()
)

Arguments

models	Optional character vector of caret model names. Defaults to all caret models.
install	Whether to install missing packages.
dependencies	Passed to install.packages().
exclude_models	Optional character vector of caret model names to skip.

Value

Invisibly returns dependency status after the attempted installation.

---

Install ugplot server dependencies

Description

Checks system dependencies required by the remote job server and installs the optional R packages used by ugPlotServer().

Usage

ugPlotInstallServerDeps(
  install = TRUE,
  dependencies = TRUE,
  install_model_deps = FALSE,
  install_geo_deps = TRUE
)

Arguments

install	Whether to install missing R packages.
dependencies	Passed to install.packages().
install_model_deps	Whether to install packages required by missing caret models too. Defaults to FALSE because this can install many packages.
install_geo_deps	Whether to install optional Bioconductor packages required for GEO methylation annotation and raw IDAT/sesame workflows.

Value

Invisibly returns a list with system and R dependency status.

---

Start a ugplot job server

Description

Starts an HTTP server that can receive datasets, run jobs in background R processes, report progress, and return completed results.

Usage

ugPlotServer(
  host = "0.0.0.0",
  port = 8080,
  jobs_dir = ugplot_default_jobs_dir(),
  token = "",
  name = "default",
  register = TRUE
)

Arguments

host	Interface to bind. Use "0.0.0.0" for remote access.
port	Port to listen on.
jobs_dir	Directory used to persist datasets, status and results.
token	Optional bearer token. Defaults to no authentication.
name	Local server handle name used by status/stop when the server is started directly.
register	Whether to write a local state file for status/stop.

Value

The plumber server result.

---

Start a ugplot job server in the background

Description

Starts ugPlotServer() in a detached R process and immediately returns control to the console.

Usage

ugPlotServerStart(
  host = "0.0.0.0",
  port = 8080,
  jobs_dir = ugplot_default_jobs_dir(),
  token = "",
  name = "default"
)

Arguments

host	Interface to bind.
port	Port to listen on.
jobs_dir	Directory used to persist datasets, status and results.
token	Optional bearer token. Defaults to no authentication.
name	Local server handle name used by status/stop.

Value

Invisibly returns the server state.

---

Get background ugplot job server status

Description

Get background ugplot job server status.

Usage

ugPlotServerStatus(name = "default", port = NULL)

Arguments

name	Local server handle name.
port	Optional port used to discover a server when no live state file is available. Defaults to the saved state port, or 8080 when there is no state.

Value

A list with server metadata and running state.

---

Stop a background ugplot job server

Description

Stop a background ugplot job server.

Usage

ugPlotServerStop(name = "default", port = NULL)

Arguments

name	Local server handle name.
port	Optional port used to discover and stop a server when no live state file is available. Defaults to the saved state port, or 8080 when there is no state.

Value

Invisibly returns TRUE when a process was stopped.

---