read.gatingML.cytobank {CytoML}R Documentation

Parser for gatingML exported by Cytobank

Description

The Default parser (flowUtils::read.gatingML) does not parse the population tree as well as the custom information from cytobank. (e.g. gate name, fcs filename).

Usage

read.gatingML.cytobank(file, ...)

Arguments

file

Gating-ML XML file

...

additional arguments passed to the handlers of 'xmlTreeParse'

Value

a graphGML that represents the population tree. The gate and population name are stored in nodeData of each node. Compensation and transformations are stored in graphData.

Examples

xml <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")
g <- read.gatingML.cytobank(xml) #parse the population tree
#plot(g) #visualize it

[Package CytoML version 1.8.1 Index]