geneSetContrastViewModule: A module to encapsulate browsing differential statistics of a...

In lianos/multiGSEA.shiny: Provides shiny components to visualize multilGSEA results

Description

The module is meant to be displayed in "a box" so that the user can examine the coherent (or not) behavior of the geneset across a contrast with respect to the background distribution of all genes in the contrast.

Usage

geneSetContrastViewUI(id, height = "590px", width = "400px")

geneSetContrastView(
  input,
  output,
  session,
  mgc,
  server = TRUE,
  maxOptions = Inf,
  sep = "_::_",
  feature.link.fn = ncbi.entrez.link,
  itools = c("wheel_zoom", "box_select", "reset", "save")
)

is.geneSetContrastViewer(x)

updateActiveGeneSetInContrastView(session, viewer, geneset, mgc)

Arguments

id	the shiny id of the module
height, width	the height and width of the module
input	the shiny-required bits for the module
output	the shiny-required bits for the module
session	the shiny-required bits for the module
mgc	A MultiGSEAResultContainer object
server	logical to indicate whether options should be loaded on the server side (default: TRUE)
maxOptions	The maximum number of options to load into the dropdown
sep	the separater to put between the collection and name bits of a geneset. These are the values used in the gene set selectizeInput.

Details

Embedded within this module is the geneSetSelect module, which provides the list of genesets the user can examine, as well as the title of the current geneset under scrutiny.

Below the geneSet picker, we embed an iplot so that the user can observe the behavior of the geneset across the contrast. The user can pick the type of plot to show (density or boxplot) as well as which statistics to use for plotting (logFC or t-statistics).

A updateActiveGeneSetInContrastView function is provided to enable interactions external to this module the ability to update the geneset selected in the geneSetSelect module.

Value

geneSetContrastViewUI returns tagList of html stuff to dump into the UI.

the geneSetContrastView module returns a reactive list, with a $gs element that indicates the currently active geneset in the 'geneSetSelect' module, and a $selected element, a character vector of feature_ids currently brushed in a contrast view.

lianos/multiGSEA.shiny documentation built on Sept. 15, 2020, 10:45 p.m.