handling processing steps in CytoPipeline objects

functions to manipulate processing steps in processing queues of CytoPipeline objects

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