Highlight the location of a particular cell population on a given bi-exponential axis.

Usage

Utility_ThirdColorPlots(
  x,
  subset,
  xaxis,
  yaxis,
  zaxis,
  splitpoint = 100,
  thecolor = "red",
  sample.name,
  removestrings,
  tilesize = 0.7,
  FactorNames = NULL,
  reference = NULL
)

Arguments

x: A GatingSet Object
subset: Desired Gate of Interest
xaxis: X-axis Marker
yaxis: Y-axis Marker
zaxis: The Marker you want visible
splitpoint: Point that denotes positive and negative for that marker.
thecolor: What color should positive cells be
sample.name: The keyword that determines a specimens name
removestrings: A list of string characters to remove from the name
tilesize: Equivalent of bin, determines the height and width of the tile dots.
FactorNames: Provide factor names when splitpoint equals categorical
reference: Provide Coereba reference when splitpoint equals crossreference

Value

A ggplot object with z-axis cells highlighted from background cells

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]
UnmixedCytoSet <- load_cytoset_from_fcs(UnmixedFCSFiles[1],
  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
#> done!
#> done.
#> Gating for 'live'
#> done!
#> done.
#> finished.

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

SinglePlot <-  Utility_ThirdColorPlots(x=UnmixedGatingSet[1],
  subset = "live", xaxis="BUV496-A", yaxis = "Spark Blue 550-A",
  zaxis ="BUV805-A", splitpoint = "continuous", sample.name = "GROUPNAME",
  removestrings = removestrings,thecolor = "blue")
#> Splitpoint is a continuous