Check gate placement for individual .fcs files in a GatingSet

Usage

Utility_GatingPlots(
  x,
  sample.name,
  removestrings,
  subset = "root",
  gtFile = NULL,
  DesiredGates = NULL,
  outpath = NULL,
  filename = NULL,
  returnType,
  bins = 270,
  therows = 2,
  thecolumns = 2,
  width = 7,
  height = 9,
  clearance = 0.2,
  optionalX = NULL,
  optionalY = NULL,
  optionalGate = NULL,
  ...
)

Arguments

x: A GatingSet object
sample.name: The .fcs keyword that contains an unique name for that sample
removestrings: A string of character values to remove from the sample.name
subset: The GatingSet subset that you want to visualize for data plotting, "root" is the default.
gtFile: The data.table imported .csv file containing the gating template.
DesiredGates: A vector of gates that you want plotted, for example Desired <- c("nonDebris, "lymphocytes")
outpath: Location to store the generated .pdf file
filename: Default NULL, overrides name
returnType: Whether to return "pdf", "patchwork" or "plots".
bins: Argument to geom_hex for number of bins to visualize the plotted data density.
therows: Number of desired rows for the .pdf file
thecolumns: Number of desired columns for the .pdf file
width: Desired page width
height: Desired page height
clearance: A buffer area around the plot edge
optionalX: When gtFile is NULL, provides x-axis argument for the subset gated population
optionalY: When gtFile is NULL, provides y-axis argument for the subset gated population
optionalGate: Default NULL, if using optional arguments and correct X and Y, the gate arg
...: Additional Arguments to NameForSample to derive filename.

Value

Additional information to be added

Examples


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)
UnstainedFCSFiles <- FCS_Files[grep("Unstained", FCS_Files)]
UnstainedCells <- UnstainedFCSFiles[-grep("Beads", UnstainedFCSFiles)]
MyCytoSet <- load_cytoset_from_fcs(UnstainedCells[1],
  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
#> done!
#> done.
#> finished.
removestrings <-  c("DR_", "Cells", ".fcs", "-", " ")
StorageLocation <- file.path("C:", "Users", "JohnDoe", "Desktop")

IndividualPlot <- Utility_GatingPlots(x=MyGatingSet[[1]],
  sample.name = "GUID",removestrings = removestrings,
  gtFile = MyGates, DesiredGates = NULL,
  outpath = StorageLocation, filename=NULL, 
  returnType = "patchwork")
#> Error in Luciernaga:::NameForSample(x = x, sample.name = sample.name,     removestrings = removestrings, ...): unused argument (filename = NULL)