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Converts the Luciernaga outputs into .pdf plots

Usage

Luciernaga_Plots(
  data,
  RetainedType,
  CellPopRatio,
  outfolder,
  filename,
  LinePlots = TRUE,
  CosinePlots = TRUE,
  StackedBarPlots = TRUE,
  HeatmapPlots = TRUE,
  returntype = "patchwork",
  reference,
  thecolumns = 2,
  therows = 2,
  width = 9,
  height = 7
)

Arguments

data

The data.frame output from LuciernagaQC

RetainedType

Whether the data.frame contains "raw" or "normalized" values

CellPopRatio

What mininum ratio needed to retain cluster.

outfolder

The location that you want to save the .pdf output to.

filename

The name you want to save your .pdf file as.

LinePlots

Passed to Utility_Patchwork for "pdf" or "patchwork" or "plots"

CosinePlots

Return this kind of plot, default is set to TRUE

StackedBarPlots

Return this kind of plot, default is set to TRUE

HeatmapPlots

Return this kind of plot, default is set to TRUE

returntype

Return "pdf", "patchwork" or "plots"

reference

path or data.frame containing Fluorophore column for ordering

thecolumns

The number of columns per page

therows

The number of rows per page

width

Desired page width

height

Desired page height

Value

A value to be determined later

Examples


library(flowCore)
library(flowWorkspace)
library(openCyto)
library(data.table)
library(dplyr)
library(purrr)
library(stringr)

File_Location <- system.file("extdata", package = "Luciernaga")
FCS_Files <- list.files(path = File_Location, pattern = ".fcs",
  full.names = TRUE)
CellSingleColorFiles <- FCS_Files[grep("Cells", FCS_Files)]
CellSingleColors <- CellSingleColorFiles[!str_detect("Unstained", CellSingleColorFiles)]
MyCytoSet <- load_cytoset_from_fcs(CellSingleColors[1:2],
  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
#> done!
#> done.
#> finished.
removestrings <-  c("DR_", "Cells", ".fcs", "-", " ")
StorageLocation <- file.path("C:", "Users", "JohnDoe", "Desktop")

FileLocation <- system.file("extdata", package = "Luciernaga")
pattern = "AutofluorescentOverlaps.csv"
AFOverlap <- list.files(path=FileLocation, pattern=pattern, full.names = TRUE)

SingleColor_Data <- map(.x=MyGatingSet[1:2], .f=Luciernaga_QC, subsets="lymphocytes",
 removestrings=removestrings, sample.name="GUID", unmixingcontroltype = "cells",
 Unstained = FALSE, ratiopopcutoff = 0.001, Verbose = FALSE, AFOverlap = AFOverlap,
 stats = "median", ExportType = "data", SignatureReturnNow = FALSE,
 outpath = TemporaryFolder, Increments=0.1, SecondaryPeaks=2,
 experiment = "FirstExperiment", condition = "ILTPanel", Subtraction = "Internal",
 CellAF=TheCellAF, SCData="subtracted", NegativeType="default") %>% bind_rows()

pattern = "^Panel.csv"
CSV <- list.files(path=FileLocation, pattern=pattern, full.names=TRUE)
TheFluorophoreOrder <- read.csv(CSV, check.names = FALSE)

ThePlots <- Luciernaga_Plots(data=SingleColor_Data, RetainedType="normalized",
 CellPopRatio=0.05, outfolder=NULL, filename="LuciernagaReport", returntype="plots",
 LinePlots=FALSE, CosinePlots=FALSE, StackedBarPlots = FALSE, HeatmapPlots = TRUE,
 reference = TheFluorophoreOrder)
#> names not matching, no reorderring according to panel order