cytobins

The goal of the cytobins package is to provide a simple tool for binning flow cytometric data, i.e. to create a data matrix of the cell counts in user-specified compartments (bins) of the space defined by any two of the detection channels (FSC, FL1, etc.). In a practical sense, this means that instead of visualizing the 2D scatter plot of those channels, the cytobins package generates a numerical matrix of customized size, equivalent of that particular plot, which facilitates further comparative mathematical analysis of flow cytometric files.

Installation

You can install the development version of cytobins from GitHub with:

# install.packages("devtools")
devtools::install_github("k-palffy/cytobins")

Usage

This package relies on the data structures defined in the R packages flowCore and flowWorkspace, as it uses GatingHierarchy objects as input. The function performing the binning procedure is cyto_binning(), which divides the ranges of two selected channels of a flow cytometric data set (a GatingHierarchy object) into n categories. The process results in a matrix with n x n compartments (bins) in the space defined by the selected channels, assigning each detected cell/event to a specific bin according to its relevant channel signals.

More info on how to use the cyto_binning() function can be found in its help file.

Example

library(flowCore)
library(flowWorkspace)
#> As part of improvements to flowWorkspace, some behavior of
#> GatingSet objects has changed. For details, please read the section
#> titled "The cytoframe and cytoset classes" in the package vignette:
#> 
#>   vignette("flowWorkspace-Introduction", "flowWorkspace")
library(cytobins)

# loading flow cytometric data of a phytoplankton sample as a GatingSet object
phyto_gs   <- load_gs(path = system.file("extdata", "phyto_flowcyt_sample", package = "cytobins"))
# creating a separate GatingHierarchy object
phyto_gh   <- phyto_gs[[1]]

# data binning along the axes of channels FSC and FL3, with 64x64 bins
# performed on a gated population ("chl") of phyto_gh
phyto_bins <- cyto_binning(gh = phyto_gh, node = "chl", channels = c(1,9),
                            xlimits = c(3,6), ylimits = c(3,7), binnumber = 64)