handling processing steps in CytoPipeline objects — handlingProcessingSteps • CytoPipeline

functions to manipulate processing steps in processing queues of CytoPipeline objects

Usage

addProcessingStep(
  x,
  whichQueue = c("scale transform", "pre-processing"),
  newPS
)

removeProcessingStep(
  x,
  whichQueue = c("scale transform", "pre-processing"),
  index
)

getNbProcessingSteps(x, whichQueue = c("scale transform", "pre-processing"))

getProcessingStep(
  x,
  whichQueue = c("scale transform", "pre-processing"),
  index
)

getProcessingStepNames(x, whichQueue = c("scale transform", "pre-processing"))

cleanProcessingSteps(
  x,
  whichQueue = c("both", "scale transform", "pre-processing")
)

showProcessingSteps(x, whichQueue = c("scale transform", "pre-processing"))

Arguments

x: a CytoPipeline object
whichQueue: selects the processing queue for which we manage the processing steps
newPS: the new processing step to be added (CytoProcessingStep object)
index: index of the processing step to remove

Value

for addProcessingStep: the updated CytoPipeline object

for removeProcessingStep: the updated CytoPipeline object

for getNbProcessingSteps: the number of processing steps present in the target queue

for getProcessingStep: the obtained CytoProcessingStep object

for getProcessingStepNames: the vector of step names

for cleanProcessingSteps: the updated CytoPipeline object

for showProcessingSteps: nothing (only console display side effect is required)

Functions

addProcessingStep(): adds a processing step in one of the processing queues (at the end), returns the modified CytoPipeline object
removeProcessingStep(): removes a processing step from one of the processing queues, returns the modified CytoPipeline object
getNbProcessingSteps(): gets the number of processing steps in a processing queue
getProcessingStep(): gets a processing step at a specific index of a processing queue
getProcessingStepNames(): gets a character vector of all processing step names of a specific processing queue
cleanProcessingSteps(): deletes all processing steps in one or both processing queues, returns the modified CytoPipeline object
showProcessingSteps(): shows all processing steps in a processing queue

Examples


rawDataDir <-
    system.file("extdata", package = "CytoPipeline")
experimentName <- "OMIP021_PeacoQC"
sampleFiles <- file.path(rawDataDir, list.files(rawDataDir,
                                             pattern = "Donor"))
transListPath <- 
    file.path(system.file("extdata", package = "CytoPipeline"), 
              "OMIP021_TransList.rds")

# main parameters : sample files and experiment name
pipelineParams <- list()
pipelineParams$experimentName <- experimentName
pipelineParams$sampleFiles <- sampleFiles

# create CytoPipeline object (no step defined yet)
pipL <- CytoPipeline(pipelineParams)

# add a processing step in scale tranformation queue
pipL <- addProcessingStep(pipL,
                          whichQueue = "scale transform",
                          CytoProcessingStep(
                              name = "scale_transform_read",
                              FUN = "readRDS",
                              ARGS = list(file = transListPath)
                          ))

getNbProcessingSteps(pipL, "scale transform") # returns 1
#> [1] 1

# add another processing step in scale transformation queue
pipL <- addProcessingStep(pipL,
                          whichQueue = "scale transform",
                          CytoProcessingStep(
                              name = "scale_transform_sum",
                              FUN = "sum",
                              ARGS = list()
                          )
)

getNbProcessingSteps(pipL, "scale transform") # returns 2
#> [1] 2

getProcessingStepNames(pipL, whichQueue = "scale transform")
#> [1] "scale_transform_read" "scale_transform_sum" 

# removes second processing step in scale transformation queue
pipL <- removeProcessingStep(pipL,
                             whichQueue = "scale transform",
                             index = 2)

# get processing step object
pS <- getProcessingStep(pipL, whichQueue = "scale transform", index = 1)
getCPSName(pS) #"scale_transform_read"
#> [1] "scale_transform_read"

# add a processing step in pre-processing queue
pipL <- addProcessingStep(pipL,
                          whichQueue = "pre-processing",
                          CytoProcessingStep(
                              name = "pre-processing_sum",
                              FUN = "sum",
                              ARGS = list()
                          ))
getNbProcessingSteps(pipL, "scale transform") # returns 1
#> [1] 1
getNbProcessingSteps(pipL, "pre-processing") # returns also 1
#> [1] 1

showProcessingSteps(pipL, whichQueue = "scale transform")
#> Scale transformations evaluation queue : 1 processing step(s)
#> 1 :Object of class "CytoProcessingStep"
#>  Name: scale_transform_read
#>  Function: readRDS
#>  Arguments:
#>   o file = /__w/_temp/Library/CytoPipeline/extdata/OMIP021_TransList.rds
showProcessingSteps(pipL, whichQueue = "pre-processing")
#> Flow frames pre-processing evaluation queue : 1 processing step(s)
#> 1 :Object of class "CytoProcessingStep"
#>  Name: pre-processing_sum
#>  Function: sum

# cleans both processing queues
pipL <- cleanProcessingSteps(pipL)
pipL
#> Pipeline object for flow cytometry experiment: OMIP021_PeacoQC 
#> Sample files: 2 sample file(s)
#> No pheno data
#> Scale transformations evaluation queue has no processing step
#> Flow frames pre-processing evaluation queue has no processing step