factor-clustering-gates.R

library(openCyto)
library(ggcyto)

create and register plugin function

tmix2DGate.wrapper <- function(fr, pp_res = NULL, channels, ...){
  res <- flowClust::flowClust(fr, varNames = channels, ...)
  #exact clustering label
  labels <- flowClust::Map(res)
  
  as.factor(labels)  
}
registerPlugins(tmix2DGate.wrapper, "tmix2DGate.wrapper")

## Registered tmix2DGate.wrapper

## [1] TRUE

the pop is set to * indicating this gating method will generate multiple gates population names are manually defined in alias and follow the same order as the gates arranged in filters container

add_pop(gs, alias = "cd4,cd8"
          , pop = "*"
          , parent = "cd3"
          , dims = "cd4,cd8"
          , gating_method = "tmix2DGate.wrapper"
          , gating_args = "K = 2, trans = 0"
          , parallel_type = "multicore"
          , mc.core = 2
          )

p <- ggcyto(gs, aes(cd4, cd8), subset = "cd3") + geom_hex() +  ggcyto_par_set(limits = "instrument")
p <- p + geom_overlay("cd4", size = 0.01, alpha = 1) + geom_overlay("cd8", color = "pink", size = 0.01, alpha = 1)
print(p)