Skip to contents

Generate NxN plots for one or all fluorophores.

Source: R/Utility_NbyNPlots.R
Utility_NbyNPlots.Rd

Generate NxN plots for one or all fluorophores.

Usage

Utility_NbyNPlots(
  x,
  sample.name,
  removestrings,
  experiment = NULL,
  experiment.name = NULL,
  condition = NULL,
  condition.name = NULL,
  marginsubset,
  gatesubset,
  ycolumn,
  bins,
  clearance,
  gatelines,
  reference = NULL,
  outpath,
  returntype,
  width = 9,
  height = 7
)

Arguments

x

A GatingSet object (ex. gs or gs[[1]])

sample.name

Keyword for which samples names are stored (ex. "GUID")

removestrings

A string of characters to remove from name ( ex. c("DR_ILT_2023_", "Cord"))

experiment

Provide directly an experiment name (ex. "Jan2024")

experiment.name

Keyword for which experiment name is stored ( ex. "GROUPNAME")

condition

Provide a condition name

condition.name

The keyword in the .fcs file storing the condition.name

marginsubset

The Gating Hierarchy level from which values will be used to estimate the plot margins (ex. "nonDebris")

gatesubset

The Gating Hierarchy level of the cells that you want to see plotted (ex. "lymph")

ycolumn

The ycolumn that you want to see everything plotted by (ex. "APC-A") or ALL to see all comparisons

bins

Bins for which the plotted cells will be divided into providing granularity

clearance

The additional ratio added to the margins to avoid clipping main population but exclude outliers.

gatelines

Whether to add estimated gate cutoff lines

reference

Reference for the gate cutoff lines

outpath

Location for which to store the generated .pdf

returntype

Whether to return as "pdf", "patchwork" or "plots"

width

Desired page width for a pdf, default is 9 inches.

height

Desired page height for a pdf, default is 7 inches

Value

A value to be determined later

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")

IndividualNxN <- Utility_NbyNPlots(x=UnmixedGatingSet[[1]],
  sample.name = "GROUPNAME", removestrings = removestrings,
  marginsubset = "lymphocytes", gatesubset = "live",
  ycolumn = "Spark Blue 550-A", bins = 70, clearance = 0.2,
  gatelines = FALSE, reference = NULL, outpath = StorageLocation,
  returntype="patchwork")
#> 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.
#> 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.
#> 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.
#> 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.
#> 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.
#> 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.
#> 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.
#> 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.
#> 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.
#> 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.
#> 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.
#> 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.
#> 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.
#> 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.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.