GOFromGatingSet: Build a gatingObj from a gatingSet

In laderast/flowDashboard: Shiny Modules for Building interactive Dashboards for flow cytometry analysis

Description

Build a gatingObj from a gatingSet

Usage

GOFromGatingSet(gs, annotation = NULL, populations = NULL,
  imageDir = NULL, mapVar = NULL, objId = NULL, makeGraphs = FALSE,
  method = "ggcyto")

Arguments

gs	- a GatingSet object.
annotation	- annotation object. if NULL, will try to pull from phenoData in gs@data
populations	- set of populations to display in data. Used in Shiny modules
imageDir	- image directory for making all gating images. Will be created if it doesn't exist.
mapVar	- a named variable that will map to populationTable.
objId	- unique ID for this object. Used in shiny modules to avoid namespace collisions.
makeGraphs	- Boolean that sets whether the function will generate all gating images The column to map in popTable is 'name'. Default value is FALSE.

Value

gatingObj

Examples

gsFile <- system.file("extdata", "gvHDgs", package="flowDashboard")
gs <- load_gs(gsFile)
tmpDir <- tempdir()
GO <- GOFromGatingSet(gs, imageDir=tmpDir, makeGraphs=TRUE)
GO

annot <- pData(gs@data@phenoData)
GO <- GOFromGatingSet(gs, annotation=annot, makeGraphs=FALSE)

laderast/flowDashboard documentation built on May 20, 2019, 7:33 p.m.