Plot the difference plot between two flow frames from a CytoPipeline run

Based on an experiment name, this function will gather the required flowFrames from the CytoPipeline disk cache and display a difference plot using the user chosen 1D or 2D view.

plotDiffFlowFrame(
  experimentNameFrom,
  experimentNameTo,
  whichQueueFrom,
  whichQueueTo,
  sampleFileFrom,
  sampleFileTo,
  path,
  flowFrameNameFrom,
  flowFrameNameTo,
  xChannelLabelFrom,
  xChannelLabelTo,
  yChannelLabelFrom,
  yChannelLabelTo,
  interactive = FALSE,
  useAllCells,
  nDisplayCells,
  useFixedLinearRange,
  linearRange,
  transfoListName = " "
)

Arguments

experimentNameFrom

the experiment name (representing a pipeline run) from which to extract the flow frame ('from' situation)

experimentNameTo

the experiment name (representing a pipeline run) from which to extract the flow frame ('to' situation)

whichQueueFrom

"pre-processing" or "scale transform" ('from' situation)

whichQueueTo

"pre-processing" or "scale transform" ('to' situation)

sampleFileFrom

in case 'whichQueueFrom' is set to 'pre-processing, which sample file to look at for the 'from' situation. This can be a number or a character.

if whichQueueFrom == "scale transform", the sampleFileFrom is ignored
if NULL and whihQueueFrom == "pre-processing", the sampleFileFrom is defaulted to the first one belonging to the experiment

sampleFileTo

same as sampleFileFrom, but for the 'to' situation

path

the root path to look for the CytoPipeline experiment cache

flowFrameNameFrom

for the 'from' situation, the name of the object to fetch (as referenced in the pipeline workflow)

flowFrameNameTo

for the 'to' situation, the name of the object to fetch (as referenced in the pipeline workflow)

xChannelLabelFrom

the label of the channel to be displayed on the x axis: the conventional syntax is : channelName + " - " + channelMarker

xChannelLabelTo

should be equal to xChannelLabelFrom (otherwise no plot is returned but NULL)

yChannelLabelFrom

the label of the channel to be displayed on the y axis: the conventional syntax is : channelName + " - " + channelMarker

yChannelLabelTo

should be equal to yChannelLabelFrom (otherwise no plot is returned but NULL)

interactive

if TRUE, uses ggplot_shiny

useAllCells

if TRUE, no subsampling will be done

nDisplayCells

if useAllCells == FALSE, the number of subsampled cells

useFixedLinearRange

if TRUE, all channels using a linear scale will use a fixed range set by linearRange

linearRange

set for all channels using a linear scale, if useFixedLinearRange == TRUE

transfoListName

if not set to " ", the transformation list (as an object name ending with "_obj", as referenced in the pipeline workflow) to be used for for display.

Value

a ggplot (or plotly if interactive = TRUE) object

Examples


# run CytoPipeline object first

outputDir <- base::tempdir()


rawDataDir <-
    system.file("extdata", package = "CytoPipeline")
experimentName <- "OMIP021_PeacoQC"
sampleFiles <- 
    file.path(
        rawDataDir, 
        list.files(rawDataDir, pattern = "Donor"))
jsonDir <- system.file("extdata", package = "CytoPipeline")
jsonPath <- file.path(jsonDir, "pipelineParams.json")

pipL2 <- CytoPipeline(
    jsonPath,
    experimentName = experimentName,
    sampleFiles = sampleFiles)

suppressWarnings(execute(
    pipL2,
    rmCache = TRUE,
    path = outputDir))
#> #####################################################
#> ### running SCALE TRANSFORMATION processing steps ###
#> #####################################################
#> Proceeding with step 1 [flowframe_read] ...
#> Proceeding with step 2 [remove_margins] ...
#> Removing margins from file : Donor1.fcs
#> Removing margins from file : Donor2.fcs
#> Proceeding with step 3 [compensate] ...
#> Compensating file : Donor1.fcs
#> Compensating file : Donor2.fcs
#> Proceeding with step 4 [flowframe_aggregate] ...
#> Proceeding with step 5 [scale_transform_estimate] ...
#> #####################################################
#> ### NOW PRE-PROCESSING FILE /__w/_temp/Library/CytoPipeline/extdata/Donor1.fcs...
#> #####################################################
#> Proceeding with step 1 [flowframe_read] ...
#> Proceeding with step 2 [remove_margins] ...
#> Removing margins from file : Donor1.fcs
#> Proceeding with step 3 [compensate] ...
#> Compensating file : Donor1.fcs
#> Proceeding with step 4 [remove_doublets] ...
#> Proceeding with step 5 [remove_debris] ...
#> Proceeding with step 6 [remove_dead_cells] ...
#> Proceeding with step 7 [perform_QC] ...
#> Applying PeacoQC method...
#> Starting quality control analysis for Donor1.fcs
#> Calculating peaks
#> MAD analysis removed 30.75% of the measurements
#> The algorithm removed 30.75% of the measurements
#> Proceeding with step 8 [transform] ...
#> #####################################################
#> ### NOW PRE-PROCESSING FILE /__w/_temp/Library/CytoPipeline/extdata/Donor2.fcs...
#> #####################################################
#> Proceeding with step 1 [flowframe_read] ...
#> Proceeding with step 2 [remove_margins] ...
#> Removing margins from file : Donor2.fcs
#> Proceeding with step 3 [compensate] ...
#> Compensating file : Donor2.fcs
#> Proceeding with step 4 [remove_doublets] ...
#> Proceeding with step 5 [remove_debris] ...
#> Proceeding with step 6 [remove_dead_cells] ...
#> Proceeding with step 7 [perform_QC] ...
#> Applying PeacoQC method...
#> Starting quality control analysis for Donor2.fcs
#> Calculating peaks
#> MAD analysis removed 24.38% of the measurements
#> The algorithm removed 24.38% of the measurements
#> Proceeding with step 8 [transform] ...


plotDiffFlowFrame(
    experimentNameFrom = experimentName,
    whichQueueFrom = "pre-processing",
    sampleFileFrom = 1,
    flowFrameNameFrom = "remove_doublets_obj",
    xChannelLabelFrom = "FSC-A : NA",
    yChannelLabelFrom = "SSC-A : NA",
    path = outputDir,
    experimentNameTo = experimentName,
    whichQueueTo = "pre-processing",
    sampleFileTo = 1,
    flowFrameNameTo = "remove_debris_obj",
    xChannelLabelTo = "FSC-A : NA",
    yChannelLabelTo = "SSC-A : NA",
    useAllCells = TRUE,
    nDisplayCells = 0,
    useFixedLinearRange = TRUE,
    linearRange = c(-100, 262144))
#> displaying flow frame comparison plot...


plotDiffFlowFrame(
    experimentNameFrom = experimentName,
    whichQueueFrom = "pre-processing",
    sampleFileFrom = 1,
    flowFrameNameFrom = "remove_doublets_obj",
    xChannelLabelFrom = "FSC-A : NA",
    yChannelLabelFrom = "SSC-A : NA",
    path = outputDir,
    experimentNameTo = experimentName,
    whichQueueTo = "pre-processing",
    sampleFileTo = 1,
    flowFrameNameTo = "remove_debris_obj",
    xChannelLabelTo = "FSC-A : NA",
    yChannelLabelTo = "SSC-A : NA",
    useAllCells = FALSE,
    nDisplayCells = 100,
    useFixedLinearRange = FALSE,
    linearRange = NULL)
#> displaying flow frame comparison plot...


plotDiffFlowFrame(
    experimentNameFrom = experimentName,
    whichQueueFrom = "pre-processing",
    sampleFileFrom = 1,
    flowFrameNameFrom = "remove_debris_obj",
    xChannelLabelFrom = "FSC-A : NA",
    yChannelLabelFrom = "Comp-525/50Violet-A : L/D Aqua - Viability",
    path = outputDir,
    experimentNameTo = experimentName,
    whichQueueTo = "pre-processing",
    sampleFileTo = 1,
    flowFrameNameTo = "remove_dead_cells_obj",
    xChannelLabelTo = "FSC-A : NA",
    yChannelLabelTo = "Comp-525/50Violet-A : L/D Aqua - Viability",
    useAllCells = TRUE,
    nDisplayCells = 0,
    useFixedLinearRange = FALSE,
    linearRange = NULL,
    transfoListName = "scale_transform_estimate_obj")   
#> displaying flow frame comparison plot...