Visualize cosine similarity of raw .fcs files to evaluate single color controls.

Usage

Luciernaga_FCSToReport(
  path,
  reference,
  stats = "median",
  LinePlots = TRUE,
  CosinePlots = TRUE,
  StackedBarPlots = TRUE,
  HeatmapPlots = TRUE,
  RetainedType,
  experiment,
  condition,
  TheSummary = TRUE
)

Arguments

path: The location to the folder where the Luciernaga .fcs files are stored
reference: A path to a .csv file or a dataframe containing Fluorophore and Detector column information for the panel.
stats: Whether to use the median or mean for fluorescent intensity.
LinePlots: Return this kind of plot, default is set to TRUE
CosinePlots: Return this kind of plot, default is set to TRUE
StackedBarPlots: Return this kind of plot, default is set to TRUE
HeatmapPlots: Return this kind of plot, default is set to TRUE
RetainedType: Whether the data.frame contains "raw" or "normalized" values
experiment: Provide directly experiment name (ex. "JAN2024")
condition: Provide directly experiment name (ex. "JAN2024")
TheSummary: Whether summarized (TRUE) or individual cells (FALSE).

Value

A data.frame compatible with LuciernagaReport()

Examples


library(flowCore)
library(flowWorkspace)
library(openCyto)
library(data.table)
library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:data.table’:
#> 
#>     between, first, last
#> The following object is masked from ‘package:flowCore’:
#> 
#>     filter
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union
library(purrr)
#> 
#> Attaching package: ‘purrr’
#> The following object is masked from ‘package:data.table’:
#> 
#>     transpose
library(stringr)

StorageLocation <- file.path(tempdir(), "LuciernagaFCSToReportExample")
if (!dir.exists(StorageLocation)) {dir.create(StorageLocation)}

File_Location <- system.file("extdata", package = "Luciernaga")
FCS_Files <- list.files(path = File_Location, pattern = ".fcs",
  full.names = TRUE)
CellSingleColorFiles <- FCS_Files[grep("Cells", FCS_Files)]
CellSingleColors <- CellSingleColorFiles[!str_detect("Unstained", CellSingleColorFiles)]
MyCytoSet <- load_cytoset_from_fcs(CellSingleColors[1:2],
  truncate_max_range = FALSE,transformation = FALSE)
MyGatingSet <- GatingSet(MyCytoSet)
MyGates <- fread(file.path(path = File_Location, pattern = 'Gates.csv'))
MyGatingTemplate <- gatingTemplate(MyGates)
#> Adding population:singletsFSC
#> Adding population:singletsSSC
#> Adding population:singletsSSCB
#> Adding population:nonDebris
#> Adding population:lymphocytes
gt_gating(MyGatingTemplate, MyGatingSet)
#> Gating for 'singletsFSC'
#> done!
#> done.
#> Gating for 'singletsSSC'
#> done!
#> done.
#> Gating for 'singletsSSCB'
#> done!
#> done.
#> Gating for 'nonDebris'
#> done!
#> done.
#> Gating for 'lymphocytes'
#> The prior specification has no effect when usePrior=no
#> Using the serial version of flowClust
#> The prior specification has no effect when usePrior=no
#> Using the serial version of flowClust
#> done!
#> done.
#> finished.
removestrings <-  c(".fcs", "(", ")", "Cells")

FileLocation <- system.file("extdata", package = "Luciernaga")
pattern = "AutofluorescentOverlaps.csv"
AFOverlap <- list.files(path=FileLocation, pattern=pattern, full.names = TRUE)

SingleColor_Data <- map(.x=MyGatingSet[1:2], .f=Luciernaga_QC,
 subsets="lymphocytes", removestrings=removestrings, sample.name="GUID",
 unmixingcontroltype = "cells", Unstained = FALSE, ratiopopcutoff = 0.001,
 Verbose = FALSE, AFOverlap = AFOverlap, stats = "median", ExportType = "fcs",
 Brightness=TRUE, SignatureReturnNow = FALSE,outpath = StorageLocation,
 Increments=0.1, SecondaryPeaks=2, experiment = "FirstExperiment",
 condition = "ILTPanel", Subtraction = "Internal", CellAF=TheCellAF,
  SCData="subtracted",NegativeType="default")

TheLuciernagaOutputs_FCS <- list.files(StorageLocation, pattern="fcs", full.names = TRUE)
TheLuciernagaOutputs_CSV <- list.files(StorageLocation, pattern="csv", full.names = TRUE)
PanelPath <- file.path(File_Location, "Panel.csv")

ReportOutput <- Luciernaga_FCSToReport(path=StorageLocation, reference=PanelPath,
 stats="median", RetainedType = "normalized", experiment="FirstExperiment",
 condition="ILTExperiment", TheSummary = TRUE)