Normalization Demo

library(flowStats)

#' load data set
gs <- load_gs(file.path(dataPath,"autoGating12"))
gs <- gs[1:4] 
plot(gs)

getNodes(gs[[1]], showHidden = T, path = "auto")

##  [1] "root"      "s1"        "s2"        "live"      "lymph"    
##  [6] "cd3"       "Bcell"     "IgDgate"   "cd27gate"  "SM"       
## [11] "UM"        "N+T"       "DN"        "MTG+"      "MTG-"     
## [16] "T1T2"      "T3"        "naiveGate" "naive"

#' cd27 marker is not aligned based on cd27gate plot
plotGate(gs, "cd27gate", type = "densityplot", stack = T)

#' normalize it within GatingSet
gs_norm <- normalize(gs
                     , target = "M+T panel_903997-25.fcs"
                     , populations = "cd27gate"
                     , dims = "<Violet A 610/20-A>"
                     , minCountThreshold = 100
                     , nPeaks = list('cd27gate' = 2)
                     , chunksize = 10
                     , bwFac = 2
                  )

## 
Estimating landmarks for channel <Violet A 610/20-A> ...
## Registering curves for parameter <Violet A 610/20-A> ...

#' results
plotGate(gs_norm, "cd27gate", type = "densityplot", stack = T)

#' normalize the underline flow data directly by flowStats:::warpSetNCDF
#' get the parent data of cd27gate
fs <- getData(gs,"Bcell")
#' run the warpSet
warped_fs <- flowStats:::warpSetNCDF(x = fs
                                     , stains = "<Violet A 610/20-A>"
                                     , peakNr = 2
                                     , target = "M+T panel_903997-25.fcs"
                                     , chunksize = 10
                                     , bwFac = 2
                                     , isNew = TRUE #Set false will write the data in place(i.e. overite the original data)
                                    )

## 
Estimating landmarks for channel <Violet A 610/20-A> ...
## Registering curves for parameter <Violet A 610/20-A> ...

#' results
grid.arrange(
  densityplot(~`cd27`, fs)
  ,densityplot(~`cd27`, warped_fs)
)