getDensities: getDensities

In saeyslab/CytoNorm: Normalisation of cytometry data measured across multiple batches

getDensities

Description

Returns a dataframe with 4 columns, containing for every file and every channel of interest the x/y values computed by density.

Usage

getDensities(
  files,
  channels,
  quantileValues = 0.5,
  transformList = NULL,
  selection = NULL,
  ...
)

Arguments

files	Full paths of to the fcs files of the samples
channels	Names of the channels to compute the densities for
quantileValues	Quantiles to extract as well
transformList	Transformation list to pass to the flowCore transform function
selection	List with indexation vector for every file.
...	Extra parameters to pass to density

Examples

dir <- system.file("extdata", package = "CytoNorm")
files <- list.files(dir, pattern = "fcs$")

ff <- flowCore::read.FCS(file.path(dir, files[1]))
channels <- grep("Di$", flowCore::colnames(ff), value = TRUE)
transformList <- flowCore::transformList(channels,
                                         cytofTransform)

densities <- getDensities(files = file.path(dir, files),
                          channels = channels,
                          transformList = transformList,
                          quantileValues = c(0.25, 0.5, 0.75))

densities$densities$Marker <- paste0(
  FlowSOM::GetMarkers(ff, densities$densities$Channel),
  " (", densities$densities$Channel, ")")

library(ggplot2)
ggplot(dplyr::filter(densities$densities,
                     File == file.path(dir, files[1]))) +
  geom_line(aes(x = x, y = y)) +
  facet_wrap(~ Marker, scales = "free") +
  theme_minimal()

ggplot(dplyr::filter(densities$quantiles,
                     Channel == FlowSOM::GetChannels(ff, "CD66"))) +
  geom_vline(aes(xintercept = `0.25`), col = "grey") +
  geom_vline(aes(xintercept = `0.5`), col = "grey", lwd = 1) +
  geom_vline(aes(xintercept = `0.75`), col = "grey") +
  geom_line(aes(x = x, y = y),
            data = dplyr::filter(densities$densities,
                     Channel == FlowSOM::GetChannels(ff, "CD66"))) +
  facet_wrap(~ File) +
  theme_minimal()

saeyslab/CytoNorm documentation built on Nov. 2, 2024, 12:39 p.m.