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Visualize Cytometry data with ggplot

Bioconductor version: Release (3.19)

With the dedicated fortify method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. ggcyto wrapper and some customed layers also make it easy to add gates and population statistics to the plot.

Author: Mike Jiang

Maintainer: Mike Jiang <mike at>

Citation (from within R, enter citation("ggcyto")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Feature summary of ggcyto HTML R Script
Quick plot for cytometry data HTML R Script
Visualize flowSet with ggcyto HTML R Script
Visualize GatingSet with ggcyto HTML R Script
Reference Manual PDF


biocViews CellBasedAssays, FlowCytometry, ImmunoOncology, Infrastructure, Software, Visualization
Version 1.32.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License file LICENSE
Depends methods, ggplot2 (>= 3.5.0), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 4.3.1)
Imports plyr, scales, hexbin, data.table, RColorBrewer, gridExtra, rlang
System Requirements
See More
Suggests testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr
Linking To
Depends On Me flowGate
Imports Me CytoML, CytoPipeline
Suggests Me CATALYST, flowCore, flowStats, flowTime, flowWorkspace, openCyto
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package ggcyto_1.32.0.tar.gz
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macOS Binary (x86_64) ggcyto_1.32.0.tgz
macOS Binary (arm64) ggcyto_1.32.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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