shinyCOMPASS: Start a Shiny Application for Visualizing COMPASS Results

In RGLab/COMPASS: Combinatorial Polyfunctionality Analysis of Single Cells

Start a Shiny Application for Visualizing COMPASS Results

Description

This function takes a COMPASSResult object, and generates a local Shiny application for visualizing the results.

Usage

shinyCOMPASS(
  x,
  dir = NULL,
  meta.vars,
  facet1 = "None",
  facet2 = "None",
  facet3 = "None",
  main = "Heatmap of Ag-Specificity Posterior Probabilities",
  stimulation = NULL,
  launch = TRUE,
  ...
)

Arguments

x	An object of class COMPASSResult.
dir	A location to write out the .rds files that will be loaded and used by the Shiny application.
meta.vars	A character vector of column names that should be used for potential facetting in the Shiny app. By default, we take all metadata variables; you may want to limit this if you know certain variables are not of interest.
facet1, facet2, facet3	Default values for facets in the Shiny app. Each should be the name of a single vector in the metadata.
main	A title to give to the heatmap and subset histogram plots.
stimulation	The name of the stimulation applied. If this is NULL, the stimulations used are inferred from the data (ie, the COMPASS call used).
launch	Boolean; if TRUE we launch the Shiny application. Otherwise, the user can launch it manually by navigating to the directory dir and running shiny::runApp().
...	Optional arguments passed to shiny::runApp.

See Also

shinyCOMPASSDeps, for identifying packages that you need in order to run the Shiny application.

Examples

if (interactive()) {
  oldOpt <- getOption("example.ask")
  options(example.ask=FALSE)
  on.exit( options(example.ask=oldOpt) )
  shinyCOMPASS(CR)
  options(example.ask=TRUE)
}

RGLab/COMPASS documentation built on Feb. 11, 2025, 4:40 p.m.