Compare the plots for given parameters for all specimens in the gating set.

Usage

Utility_UnityPlot(
  x,
  y,
  GatingSet,
  marginsubset,
  gatesubset,
  sample.name,
  removestrings,
  clearance,
  bins,
  gatelines,
  reference,
  returntype,
  outpath
)

Arguments

x: The desired x-axis parameter
y: The desired y-axis parameter
GatingSet: The Gating Set that contains the specimens
marginsubset: The desired gate for the margins
gatesubset: The desired gate of cells you want to plot
sample.name: The keyword that designates different specimens
removestrings: Values to remove from both the plot titles and the pdf
clearance: A value of clearance multiplied to the margin
bins: How many bins to class the cells into
gatelines: Whether to plot the reference lines
reference: A data.frame containing references
returntype: Whether to return "pdf", "patchwork" or "plots"
outpath: The desired location to send the assembled pdf to

Value

The ggplots for all the specimens, as well as the optional .pdf

Examples


library(BiocGenerics)
library(flowCore)
library(flowWorkspace)
library(openCyto)
library(data.table)

File_Location <- system.file("extdata", package = "Luciernaga")
FCS_Files <- list.files(path = File_Location, pattern = ".fcs",
  full.names = TRUE)
Unmixed_FullStained <- FCS_Files[grep("Unmixed", FCS_Files)]
UnmixedFCSFiles <- Unmixed_FullStained[1:2]
UnmixedCytoSet <- load_cytoset_from_fcs(UnmixedFCSFiles[1:2],
  truncate_max_range = FALSE,transformation = FALSE)
UnmixedGatingSet <- GatingSet(UnmixedCytoSet)
Markers <- colnames(UnmixedCytoSet)
KeptMarkers <- Markers[-grep("Time|FS|SC|SS|Original|-W$|-H$|AF", Markers)]
MyBiexponentialTransform <- flowjo_biexp_trans(channelRange = 256,
  maxValue = 1000000,pos = 4.5, neg = 0, widthBasis = -1000)
TransformList <- transformerList(KeptMarkers, MyBiexponentialTransform)
UnmixedGatingSet <- flowWorkspace::transform(UnmixedGatingSet, TransformList)
FileLocation <- system.file("extdata", package = "Luciernaga")
UnmixedGates <- fread(file.path(path = FileLocation, pattern = 'GatesUnmixed.csv'))
UnmixedGating <- gatingTemplate(UnmixedGates)
#> Adding population:singletsFSC
#> Adding population:singletsSSC
#> Adding population:singletsSSCB
#> Adding population:nonDebris
#> Adding population:lymphocytes
#> Adding population:live
gt_gating(UnmixedGating, UnmixedGatingSet)
#> 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.
#> Gating for 'live'
#> done!
#> done.
#> finished.

removestrings <-  c("DTR_", ".fcs")
StorageLocation <- file.path("C:", "Users", "JohnDoe", "Desktop")

SingleUnityPlot <- Utility_UnityPlot(x="Spark Blue 550-A", y="BUV805-A",
GatingSet=UnmixedGatingSet, sample.name="GROUPNAME", bins=100, clearance=0.2,
removestrings=removestrings, marginsubset="lymphocytes", gatesubset="live",
gatelines=FALSE, reference=NULL, returntype="patchwork",outpath=StorageLocation)
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.