flowQuick

Quick and reproducible flow cytometry analysis in R.

flowQuick provides convenience wrappers around the Bioconductor flow cytometry stack (flowCore, flowWorkspace, flowAI and ggcyto) so that a typical analysis — quality control, compensation, scatter/singlet gating, fluorescence-minus-one (FMO) gating and plotting — takes a handful of calls instead of pages of boilerplate.

A small example data set (cs, a cytoset borrowed from a real experiment) is bundled so you can try every function without any FCS files of your own.

Installation

# install.packages("remotes")
remotes::install_github("jonesnoaht/flowQuick")

flowQuick depends on several Bioconductor packages. If they are not already installed:

# install.packages("BiocManager")
BiocManager::install(c("flowCore", "flowWorkspace", "flowAI", "ggcyto",
                       "flowStats", "CytoML", "cytolib"))

Quick start

library(flowQuick)

# 1. Read raw FCS files into a flowSet
fs <- generate_flowset("path/to/fcs/files")

# 2. Quality-control the data (runs flowAI, caches the result on disk)
cs <- get_fcs_resultsQC(QC_folder = "resultsQC/", raw_folder = "rawData/")

# 3. Build a GatingSet with tube names attached
gs <- make_gs(cs)

# 4. Add cell + singlet gates in one call (safe to re-run)
gates <- quick_gate(gs)

# 5. Draw gates automatically from your FMO controls
make_gates_from_fmos(gs, parent = "SSC-singlet", search_term = "FMO")

# 6. Hand the gates off to FlowJo (and read them back later)
gs_to_flowjo(gs, "my_analysis.wsp")
gs2 <- flowjo_to_gs("my_analysis.wsp")

Automatic FMO gating

make_gates_from_fmos() finds the FMO control tubes (by search_term), works out which marker each is the FMO for, and draws a one-dimensional threshold gate for that marker across every sample. By default the negative/positive cutoff is a robust upper fence, median + k * mad, which is less sensitive to the spread of the FMO population than a raw percentile. Pass method = "quantile" to use a high quantile instead:

# Robust default (median + 5 * MAD)
make_gates_from_fmos(gs, parent = "SSC-singlet")

# Looser robust gate
make_gates_from_fmos(gs, parent = "SSC-singlet", k = 3)

# Quantile-based cutoff at the 99.9th percentile
make_gates_from_fmos(gs, parent = "SSC-singlet",
                     method = "quantile", probability = 0.999)

Function reference

Function	What it does
generate_flowset()	Read every .fcs file in a folder into a flowSet.
get_fcs_resultsQC()	Load cached QC results, or run flowAI QC if none exist.
compensate_data()	Build a spillover matrix from single-stained controls.
make_gs()	Turn a cytoset into a GatingSet with tube names in pData.
quick_gate()	Add cell, FSC-singlet and SSC-singlet gates (idempotent).
set_scatter_gate()	Add an arbitrary polygon gate from raw coordinates.
test_plot()	Preview a polygon gate before committing to it.
make_gates_from_fmos()	Automatically derive positive/negative gates from FMO controls.
update_gate()	Replace an existing gate's filter in place.
gs_to_flowjo()	Export a GatingSet to a FlowJo workspace (.wsp).
flowjo_to_gs()	Read a FlowJo .wsp workspace back into a GatingSet.

clean_data() is retained for backwards compatibility but is deprecated in favour of get_fcs_resultsQC().

For a full, end-to-end walk-through (QC → compensation → gating → publication figures) see the example vignette.

License

MIT © flowQuick authors. See LICENSE.md.