In DillonHammill/CytoGate: openCyto Plugin Gating Functions

CytoGate

Plugin Gating Functions for openCyto

Installation

CytoGate can be installed from Github

GitHub

library(devtools)
install_github("DillonHammill/CytoGate")

Plugin Example

To demonstrate the use of CytoGate the following example uses the gate_draw plugin for openCyto to draw polygonGates manually using the mouse.

Register openCyto Plugin

library(openCyto)
library(CytoGate)

registerPlugins(fun = gate_draw, methodName = "DrawGate")
listgtMethods()

Construct GatingSet

data(Activation, package = "CytoGate")
gs <- GatingSet(Activation)

trans <- estimateLogicle(gs[[1]], "SSC-A")
gs <- transform(gs, trans)

Construct GatingTemplate Entry

library(flowDensity)

template <- add_pop(
gs, alias = "Lymphocytes", pop = "+", parent = "root", dims = "FSC-A,SSC-A", 
gating_method = "DrawGate", gating_args = "subSample=20000", collapseDataForGating = TRUE,
groupBy = 2
)

Plot Gating Result

library(ggcyto)
ggcyto(gs, subset = "root", aes(x = "FSC-A", y = "SSC-A")) + geom_hex(bins = 100) + geom_gate("Lymphocytes") + geom_stats()

Dillon Hammill, BMedSci (Hons)
Ph.D. Scholar
The Parish Group – Cancer & Vascular Biology
ACRF Department of Cancer Biology and Therapeutics
The John Curtin School of Medical Research
ANU College of Medicine, Biology and the Environment
The Australian National University
Acton ACT 2601
[e-mail]

DillonHammill/CytoGate documentation built on May 16, 2019, 7:20 a.m.