In Silico Treatment Modelling Browser

The purpose of this R package is to provide an interactive shiny app to browse results generated with the In Silico Treatment IST R package.

Overview

Filter page (landing page), where one can filter and compare signatures

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Compare page, where one can compare two signatures

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Prioritise page, where one can prioritise signatures across pathways, or pathways across signatures

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Data overview tab, where one can browse the bare bones data for gene sets and signatures (under construction)

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Requirements

The IST package must be installed to run this browser. This app only needs an ist.results object saved as a .rds file, with some extra required fields in the sample and pathway metadata.

A pathways.meta data.frame has to be defined, when creating the ist.pathways object, with at least the following columns with pathway metadata:

• path.id: character, names as in the pathway data frame
• path.class: character, either "default" to show in the app loading page, or something else

The signature metadata, as provided in tab.meta for the ist.signatures object, must include two extra columns

• sig.class: character, "default", "positivecontrol", or something else
• study.id: character, anything, for fill colors in the boxplot

Usage

• Load package: Ctrl/Cmd + Shift + L
• Launch application: ISTBrowser::run()

or:

devtools::load_all()
ISTBrowser::run()

Deployment

Development

Assuming code is checked out in ~/ISTBrowser, create application bootstrap script ~/ShinyApps/istbrowser/app.R:

shinyOptions(ist.result.path = "/path/to/ist/results/rds/file.rds")
shinyOptions(ist.browser.title = "Idiopathic Pulmonary Fibrosis")
devtools::load_all(paste(Sys.getenv("HOME"), "ISTBrowser", sep="/"))
shiny::shinyAppDir(system.file("app", package = "ISTBrowser"))

For testing purposes, one can use the sample object that comes in the IST package, IST::sample.results.ist, save as a .rds file, and load it with the app.

Production

Create application bootstrap script app.R:

shinyOptions(ist.result.path = "/path/to/ist/results/rds/file.rds")
shinyOptions(ist.browser.title = "Idiopathic Pulmonary Fibrosis")
shinyOptions(ist.browser.description = "Comparison of disease models for IPF.")
shiny::shinyAppDir(system.file("app", package = "ISTBrowser"))