Title: A Configurable 'shiny' Portal for Sharing Analysis of Molecular Expression Data
Version: 1.2.1
Maintainer: Rafael Henkin <r.henkin@qmul.ac.uk>
Description: Enables deploying configuration file-based 'shiny' apps with minimal programming for interactive exploration and analysis showcase of molecular expression data. For exploration, supports visualization of correlations between rows of an expression matrix and a table of observations, such as clinical measures, and comparison of changes in expression over time. For showcase, enables visualizing the results of differential expression from package such as 'limma', co-expression modules from 'WGCNA' and lower dimensional projections.
Depends: R (≥ 3.5.0)
License: MIT + file LICENSE
Imports: config, stats, utils, shiny, htmltools, markdown, cli, dplyr, tidyr, yaml, data.table, bslib, iheatmapr, vegawidget, DT, qvalue, parallel, Rfast, rlang, shinyhelper
Encoding: UTF-8
RoxygenNote: 7.3.2
Suggests: testthat (≥ 3.0.0), whisker, knitr, rmarkdown, r2d3, kableExtra, RColorBrewer
VignetteBuilder: knitr
URL: https://c4tb.github.io/shinyExprPortal/, https://github.com/C4TB/shinyExprPortal
Config/testthat/edition: 3
BugReports: https://github.com/C4TB/shinyExprPortal/issues
NeedsCompilation: no
Packaged: 2024-07-29 12:54:52 UTC; rafaelhenkin
Author: Rafael Henkin ORCID iD [cre, aut, cph]
Repository: CRAN
Date/Publication: 2024-07-29 15:10:02 UTC

Create a bare-bones configuration file template

Description

The resulting file contain placeholder text in upper case for you to edit according to your needs. It also includes the three correlation modules by default.

Usage

create_config_template(target_dir, filename = "config.yaml")

Arguments

target_dir

location to create the configuration file

filename

optional file name, default is config.yaml

Value

Creates configuration file in target_dir

Examples

if (interactive()) {
    dir.create("newapp")
    create_config_template("newapp")
}

Create configuration and app.R files

Description

This function runs an interactive wizard that guides the user through the creation of a basic configuration file. The wizard will work with the simple case of expression data where one sample matches exactly to one subject.

Usage

create_config_wizard(target_dir)

Arguments

target_dir

location where the configuration will be saved

Details

Before you run the wizard, you should ensure that the target folder contains at least the expression matrix and measures data files. The expression matrix should follow the format of sample IDs in columns and genes in rows, with gene names in the first column of the table. The measures file should follow the format of subjects in rows and measures in columns, and you should ensure that all subjects have one sample and vice-versa.

Value

Creates configuration file in target_dir

Examples

if (interactive()) {
    dir.create("newapp")
    create_config_wizard("newapp")
}

Create example files

Description

Create example files for measures, expression matrix and lookup table

Usage

create_example(target_dir)

Arguments

target_dir

location where to create the files

Value

Create examples files in target_dir

Examples

if (interactive()) {
    dir.create("newapp")
    create_example("newapp")
}

Creates a module code template in current working directory

Description

Creates a module code template in current working directory

Usage

create_module_template(module_name, target_dir = "")

Arguments

module_name

module name in camelCase

target_dir

Optional folder where to save the file. Saves in current folder otherwise.

Value

Create file for module_name in current working directory

Examples

if (interactive()) {
    create_module_template("newModule")
}

Run the Shiny Application

Description

This function should be run only after you have created the configuration file and placed all required files in the app folder. See vignette("quickstart", package = "shinyExprPortal") for help with setup or vignette("fullguide", package = "shinyExprPortal") for a complete configuration guide.

Usage

run_app(
  config_file,
  data_folder = "",
  custom_modules = NULL,
  nthreads = 1L,
  ...
)

Arguments

config_file

The name of the yaml configuration file

data_folder

Optional directory prefix for data files. Use this argument if you want to version your files across different folders

custom_modules

Optional list of available custom modules. See the 'Details' section.

nthreads

Optional number of threads/cores to speed up loading files and computing correlations on UNIX-based systems. Default is 1

...

Further optional arguments.

Details

custom_modules should contain a list of names for user-defined modules that are loaded in the environment before calling run_app. Each module should be accompanied by the corresponding mod_moduleName_ui, mod_moduleName_server moduleName_config functions. These functions could be placed in a custom_modules.R file, for example, and loaded using source. The package will then parse the configuration file, and if it contains one of the custom module names, it will call the module configuration parsing function and add it to the interface. See vignette("customization") for a complete example.

Please note that if running on Windows, nthreads will be always set to 1 due to limitations on the current implementation.

Value

Runs the app

See Also

create_config_wizard() to create a configuration using a wizard, create_config_template() to create a configuration file template.

Examples

if (interactive()) {
run_app("config.yaml", nthreads = 4)
}

Print list of currently supported modules

Description

See vignette("config", package = "shinyExprPortal") for details on how to configure each module.

Usage

show_available_modules()

Value

list of available modules

Examples

show_available_modules()