ApplyGate: ApplyGate

In Mthrun/dbt.FlowCytometry: Databionics Toolbox for the Analysis of Fluorescence-Activated Cell Sorting (FACS) Data

ApplyGate

Description

A specific Gate defined by xy coordinates that result in a closed polygon is applied to the flowcytometry data.

Usage

ApplyGate(Data, GateVar1, GateVar2, Polygon, PlotIt = FALSE, PlotSampleSize = 1000)

Arguments

Data	numerical matrix n x d
GateVar1	either column index in Data of X coordinate of gate or its variable name as string
GateVar2	either column index in Data of X coordinate of gate or its variable name as string
Polygon	numerical marix of two columns defining the coordiantes of the polygon. polygon assumed to be closed, i.e.,last coordinate connects to first coordinate.
PlotIt	if TRUE: plots a sample of data in the two selected variables and marks point inside the gate as yellow and outside as magenta
PlotSampleSize	size pof the plottet sample

Details

Gates are alwaxs two dimensional, i.e., require two filters, although all dimensions of data are filted by the gates. Only high-dimensional points inside the polygon (gate) are given back

Value

list of

DataInGate	m x d numerical matrix with m<=n of data points inside the gate
InGateInd	index of length m for the datapoints in original matrix

Note

if GateVar1 or GateVar2 is not found a text is given back which will state this issue

Author(s)

Michael Thrun

See Also

PointsInPolygon

Examples

Data <- matrix(runif(1000), ncol = 10)
colnames(Data)=paste0("GateVar",1:ncol(Data))
poly <- cbind(x = c(0.2,0.5,0.8), y = c(0.2,0.8,0.2))
#set plotit TRUE for understanding the example

#Select indect
V=ApplyGate(Data,5,8,poly,PlotIt=FALSE,100)

#select var name
V=ApplyGate(Data,"GateVar5","GateVar8",poly,PlotIt=FALSE,100)

Mthrun/dbt.FlowCytometry documentation built on June 5, 2023, 10:30 a.m.