Generates cosine comparison from a data.frame of fluorescent signatures

Usage

Luciernaga_Cosine(
  data,
  returntype = "plot",
  rearrange = TRUE,
  colorlow = "lightblue",
  colorhigh = "red",
  limitlow = 0.4,
  limithigh = 1,
  legend = TRUE
)

Arguments

data: A data.frame with a single name column and rest numeric columns
returntype: Default returns "plot", alternatively "data" for underlying data
rearrange: Whether to rearrange the plot to group similar signatures
colorlow: Default "lightblue"
colorhigh: Default "orange"
limitlow: Default 0.4
limithigh: Default 1
legend: Default TRUE

Value

Either a ggplot or matrix object

Examples


library(flowCore)
library(flowWorkspace)
library(openCyto)
library(data.table)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:data.table':
#> 
#>     between, first, last
#> The following object is masked from 'package:flowCore':
#> 
#>     filter
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

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")

PopulationInterest <- gs_pop_get_data(MyGatingSet[1], subset="lymphocytes")
TheDataValues <- exprs(PopulationInterest[[1]])
TheDataValues <- data.frame(TheDataValues, check.names=FALSE)
Signature <- AveragedSignature(TheDataValues, stats="median")
TheData1 <- Signature[,-grep("Time|FS|SC|SS|Original|W$|H$", names(Signature))]
TheData1 <- TheData1 %>% mutate(Sample="lymphocytes") %>%
 relocate(Sample, .before=1)

PopulationInterest <- gs_pop_get_data(MyGatingSet[1], subset="nonDebris")
TheDataValues <- exprs(PopulationInterest[[1]])
TheDataValues <- data.frame(TheDataValues, check.names=FALSE)
Signature <- AveragedSignature(TheDataValues, stats="median")
TheData2 <- Signature[,-grep("Time|FS|SC|SS|Original|W$|H$", names(Signature))]
TheData2 <- TheData2 %>% mutate(Sample="nonDebris") %>%
 relocate(Sample, .before=1)

FinalData <- rbind(TheData1, TheData2)

Plot <- Luciernaga_Cosine(data=FinalData, returntype="plot")