non-geom-gate.R

library(openCyto)
library(ggcyto)

load data

data(GvHD)
fs <- GvHD[1:2]
gs <- GatingSet(fs)

Before the time gate

autoplot(fs, x = "time", y = "SSC-H", bins = 64)

create timeFilters

tf <- timeFilter("SSC-H", bandwidth=0.5, filterId="myTimeFilter")

it is not a geometrical gate thus can not be added to gatingset directly

tf

## time filter 'myTimeFilter' with settings:
##   bandwidth=0.5

but we do support adding the logicalFilterResult as a special logicalGate

fres <- filter(fs, tf)
fres

## A list of filterResults for a flowSet containing 2 frames
## produced by the filter named 'myTimeFilter'

is(fres[[1]], "logicalFilterResult")

## [1] TRUE

add(gs, fres, name = "time gate", parent = "root")

## NULL

getNodes(gs)

## [1] "root"       "/time gate"

Visualizing the cleaned data

cleaned <- getData(gs, "time gate")
autoplot(cleaned, x = "time", y = "SSC-H", bins = 64)

## Warning: Removed 78 rows containing missing values (geom_hex).

Or visualize the gate as overlay dots

ggcyto(gs, aes(x = "time", y = "SSC-H")) + geom_hex() + geom_gate("time gate")

## Warning: Removed 107 rows containing missing values (geom_hex).

Create a plugin wrapper function that returns a filterResult object

myTimeGate <- function(fr, pp_res = NULL, channels, ...){
  tf <- timeFilter(channels, ...)
  fres <- filter(fr, tf)
  return(fres)
}
registerPlugins(myTimeGate, "timeGate")

## Registered timeGate

## [1] TRUE

now timeGate is ready to be used in openCyto template