Runs UMAP (uwot implementation)

Usage

Utility_UMAP(
  x,
  sample.name,
  removestrings,
  subset,
  columns = NULL,
  notcolumns = NULL,
  subsample = NULL,
  export = FALSE,
  outpath = NULL,
  metric = "euclidean",
  n_neighbors = 15,
  min_dist = 0.5,
  ...
)

Arguments

x: A gating set object
sample.name: Keyword for which sample name is stored
removestrings: A list of things to remove from sample.name
subset: The subset of interest from gating hierarchy
columns: Which columns to use. Not combinable with notcolumns, use one or other.
notcolumns: Which columns not to use. Not combinable with columns, use one or other.
subsample: If downsampling is wanted.
export: When set to TRUE returns fcs files to specified outpath.
outpath: Location to store new .fcs files
metric: umap Argument, default is set to "euclidean"
n_neighbors: umap Argument, default is set to 15
min_dist: umap Argument, default is set to 0.5
...: Other arguments to pass to umap()

Value

UMAP axes bound to a flowframe or fcs file

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")

Markers <- colnames(UnmixedCytoSet)
KeptMarkers <- Markers[-grep("Time|FS|SC|SS|Original|-W$|-H$|AF", Markers)]
SubsetMarkers <- c("BUV496-A", "BUV805-A", "Pacific Blue-A", "BV711-A",
  "BV786-A", "Spark Blue 550-A", "PE-A", "APC-Fire 750-A")

UMAP_Output <- Utility_UMAP(x=UnmixedGatingSet[[1]], sample.name="GUID",
  removestrings=c("_Cells", ".fcs"), subset="nonDebris",
  columns=KeptMarkers, export=FALSE)