extend: extend the gate to the minimum and maximum limit of both...

In CytoML: A GatingML Interface for Cross Platform Cytometry Data Sharing

Description

It is equivalent to the behavior of shifting the off-scale boundary events into the gate boundary that is describled in bounding transformation section of gatingML standard.

Usage

extend(
  gate,
  bound,
  data.range = NULL,
  plot = FALSE,
  limits = c("original", "extended")
)

## S3 method for class 'polygonGate'
extend(
  gate,
  bound,
  data.range = NULL,
  plot = FALSE,
  limits = c("original", "extended")
)

## S3 method for class 'rectangleGate'
extend(gate, ...)

## S3 method for class 'ellipsoidGate'
extend(gate, ...)

Arguments

gate	a flowCore filter/gate
bound	numeric matrix representing the bouding information parsed from gatingML. Each row corresponds to a channel. rownames should be the channel names. colnames should be c("min", "max")
data.range	numeric matrix specifying the data limits of each channel. It is used to set the extended value of vertices and must has the same structure as 'bound'. when it is not supplied, c(-.Machine$integer.max, - .Machine$integer.max) is used.
plot	whether to plot the extended polygon.
limits	character whether to plot in "extended" or "original" gate limits. Default is "original".
...	other arguments

Details

The advantage of extending gates instead of shifting data are two folds: 1. Avoid the extra computation each time applying or plotting the gates 2. Avoid changing the data distribution caused by adding the gates

Normally this function is not used directly by user but invoked when parsing GatingML file exported from Cytobank.

Value

a flowCore filter/gate

Examples

library(flowCore)
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", sqrcut)
pg
bound <- matrix(c(100,3e3,100,3e3), 
    byrow = TRUE, nrow = 2, 
   dimnames = list(c("FSC-H", "SSC-H"), 
     c("min", "max")))
bound
pg.extened <- extend(pg, bound, plot = TRUE)

CytoML documentation built on March 12, 2021, 2 a.m.