ggcyto

This is the development version of ggcyto; for the stable release version, see ggcyto.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

Visualize Cytometry data with ggplot

Bioconductor version: Development (3.24)

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 ozette.com>

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

Mike Jiang. ggcyto: Visualize Cytometry data with ggplot. doi:10.18129/B9.bioc.ggcyto, R package version 1.41.1, https://bioconductor.org/packages/ggcyto.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("ggcyto")

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

Documentation

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

browseVignettes("ggcyto")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBasedAssays, FlowCytometry, ImmunoOncology, Infrastructure, Software, Visualization
Version	1.41.1
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 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, BiocGenerics (>= 0.59.5)
System Requirements
URL	https://github.com/RGLab/ggcyto/issues

Suggests	testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr
Linking To
Enhances
Depends On Me	flowGate
Imports Me	CompensAID, CytoML, CytoPipeline
Suggests Me	CATALYST, CyFj11, flowCore, flowStats, flowTime, flowWorkspace, openCyto, staRgate
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ggcyto_1.41.1.tar.gz
Windows Binary (x86_64)	ggcyto_1.41.1.zip
macOS Binary (big-sur-x86_64)	ggcyto_1.41.1.tgz
macOS Binary (sonoma-arm64)	ggcyto_1.41.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ggcyto
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ggcyto
Package Short Url	https://bioconductor.org/packages/ggcyto/
Package Downloads Report	Download Stats