In primitybio/cellengine-r-toolkit: 'CellEngine' API Toolkit

Converting flowDensity gates:

flowDensity gates can be converted to CellEngine gates. The class of a flowDensity gate is "CellPopulation". The flowDensity@filter is always a polygon, so cellengine::createPolygonGate can be used for this purpose:

file = "sample1.fcs"
flowDensityGate <- flowDensity::flowDensity(file, params)@filter
experimentId <- "5d2f8b4b21fd0676fb3a6a8c"

polyGate <- createPolygonGate(
    experimentId,
    colnames(flowDensityGate)[1],
    colnames(flowDensityGate)[2],
    name,
    vertices = list(flowDensityGate),
)

As a function:

convertFlowDensity <- function(flowDensityOutput, experimentId, name = NULL, ...) {
  flowDensityGate <- flowDensityOutput@filter
  createPolygonGate(
    experimentId,
    colnames(flowDensityGate)[1],
    colnames(flowDensityGate)[2],
    name,
    vertices = list(flowDensityGate),
    ...
  )
}