Generate the plots into a single pdf

Usage

Utility_Patchwork(
  x,
  filename,
  outfolder,
  thecolumns = 2,
  therows = 3,
  width = 7,
  height = 9,
  returntype = "pdf",
  NotListofList = TRUE
)

Arguments

x: A list of plots
filename: Name to save the .pdf as
outfolder: Location to save the .pdf
thecolumns: The number of columns per page
therows: The number of rows per page
width: Desired page width
height: Desired page height
returntype: Whether to return "pdf" (to desired location) or "patchwork" (to R)
NotListofList: Internal default is True, don't touch.

Value

Some additional value to edit

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[1:3],
  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
#> 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")

AllSpecimens <- Utility_IterativeGating(x=MyGatingSet[1:3],
 sample.name = "GUID", removestrings = removestrings,
 subset = "nonDebris", gate = "lymphocytes", xValue = "FSC-A",
  yValue = "SSC-A", bins = 270)

Patchwork <- Utility_Patchwork(AllSpecimens, "LymphocyteGates",
 outfolder=StorageLocation, thecolumns=2, therows=2,
  width = 7, height = 9, returntype="patchwork")