Class

Class and constructor for 2-dimensional polygonal filter objects.

polygonGate(..., .gate, boundaries, filterId="defaultPolygonGate")

Arguments

filterId	An optional parameter that sets the `filterId` of this gate.
.gate, boundaries	A definition of the gate. This can be either a list or a named matrix as described below. Note the argument boundaries is deprecated and will go away in the next release.
...	You can also directly describe a gate without wrapping it in a list or matrix, as described below.

Value

Returns a polygonGate object for use in filtering flowFrames or other flow cytometry objects.

Details

Polygons are specified by the coordinates of their vertices in two dimensions. The constructor is designed to be useful in both direct and programmatic usage. It takes either a list or a named matrix with 2 columns and at least 3 rows containing these coordinates. Alternatively, vertices can be given as named arguments, in which case the function tries to convert the values into a matrix.

Slots

boundaries

Object of class "matrix". The vertices of the polygon in two dimensions. There need to be at least 3 vertices specified for a valid polygon.

parameters

Object of class "character", describing the parameter used to filter the flowFrame.

filterId

Object of class "character", referencing the filter.

Note

See the documentation in the flowViz package for plotting of polygonGates.

Extends

Class "parameterFilter", directly.

Class "concreteFilter", by class parameterFilter, distance 2.

Class "filter", by class parameterFilter, distance 3.

Objects from the Class

Objects can be created by calls of the form new("polygonGate", ...) or by using the constructor polygonGate. Using the constructor is the recommended way.

Methods

%in%

signature(x = "flowFrame", table = "polygonGate"): The workhorse used to evaluate the filter on data. This is usually not called directly by the user, but internally by calls to the filter methods.

show

signature(object = "polygonGate"): Print information about the filter.

Examples


## Loading example data
dat <- read.FCS(system.file("extdata","0877408774.B08",
package="flowCore"))

## Defining the gate
sqrcut <- matrix(c(300,300,600,600,50,300,300,50),ncol=2,nrow=4)
colnames(sqrcut) <- c("FSC-H","SSC-H")
pg <- polygonGate(filterId="nonDebris", boundaries= sqrcut)
#> Warning: The 'boundaries' argument is deprecated, please use '.gate' instead.
pg
#> Polygonal gate 'nonDebris' with 4 vertices in dimensions FSC-H and SSC-H

## Filtering using polygonGates
fres <- filter(dat, pg)
fres
#> A filterResult produced by the filter named 'nonDebris'
summary(fres)
#> nonDebris+: 6680 of 10000 events (66.80%)

## The result of polygon filtering is a logical subset
Subset(dat, fres)
#> flowFrame object '0877408774.B08'
#> with 6680 cells and 8 observables:
#>      name              desc range minRange maxRange
#> $P1 FSC-H             FSC-H  1024 0.000000     1023
#> $P2 SSC-H             SSC-H  1024 0.000000     1023
#> $P3 FL1-H              <NA>  1024 1.009044    10000
#> $P4 FL2-H              <NA>  1024 1.009044    10000
#> $P5 FL3-H              <NA>  1024 1.009044    10000
#> $P6 FL1-A              <NA>  1024 0.000000     1023
#> $P7 FL4-H              <NA>  1024 1.009044    10000
#> $P8  Time Time (51.20 sec.)  1024 0.000000     1023
#> 164 keywords are stored in the 'description' slot

## We can also split, in which case we get those events in and those
## not in the gate as separate populations
split(dat, fres)
#> $`nonDebris+`
#> flowFrame object '0877408774.B08 (nonDebris+)'
#> with 6680 cells and 8 observables:
#>      name              desc range minRange maxRange
#> $P1 FSC-H             FSC-H  1024 0.000000     1023
#> $P2 SSC-H             SSC-H  1024 0.000000     1023
#> $P3 FL1-H              <NA>  1024 1.009044    10000
#> $P4 FL2-H              <NA>  1024 1.009044    10000
#> $P5 FL3-H              <NA>  1024 1.009044    10000
#> $P6 FL1-A              <NA>  1024 0.000000     1023
#> $P7 FL4-H              <NA>  1024 1.009044    10000
#> $P8  Time Time (51.20 sec.)  1024 0.000000     1023
#> 164 keywords are stored in the 'description' slot
#> 
#> $`nonDebris-`
#> flowFrame object '0877408774.B08 (nonDebris-)'
#> with 3320 cells and 8 observables:
#>      name              desc range minRange maxRange
#> $P1 FSC-H             FSC-H  1024 0.000000     1023
#> $P2 SSC-H             SSC-H  1024 0.000000     1023
#> $P3 FL1-H              <NA>  1024 1.009044    10000
#> $P4 FL2-H              <NA>  1024 1.009044    10000
#> $P5 FL3-H              <NA>  1024 1.009044    10000
#> $P6 FL1-A              <NA>  1024 0.000000     1023
#> $P7 FL4-H              <NA>  1024 1.009044    10000
#> $P8  Time Time (51.20 sec.)  1024 0.000000     1023
#> 164 keywords are stored in the 'description' slot
#>

Class "polygonGate"