README.md

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)

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
)

## Select at least 3 points to construct a polygon gate around the population.

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.