ggcyto

DOI: 10.18129/B9.bioc.ggcyto    

Visualize Cytometry data with ggplot

Bioconductor version: Release (3.14)

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 <wjiang2 at fhcrc.org>,Jake Wagner <jpwagner at fhcrc.org>

Installation

To install this package, start R (version "4.1") and enter:

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

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")

 

HTML	R Script	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
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBasedAssays, FlowCytometry, ImmunoOncology, Infrastructure, Software, Visualization
Version	1.22.0
In Bioconductor since	BioC 3.3 (R-3.3) (6 years)
License	Artistic-2.0
Depends	methods, ggplot2 (>= 3.3.0), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 3.33.1)
Imports	plyr, scales, hexbin, data.table, RColorBrewer, gridExtra, rlang
LinkingTo
Suggests	testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr
SystemRequirements
Enhances
URL	https://github.com/RGLab/ggcyto/issues
Depends On Me
Imports Me	CytoML
Suggests Me	CATALYST, flowCore, flowStats, flowTime, flowWorkspace, openCyto
Links To Me
Build Report

Package Archives

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

Source Package	ggcyto_1.22.0.tar.gz
Windows Binary	ggcyto_1.22.0.zip
macOS 10.13 (High Sierra)	ggcyto_1.22.0.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
Old Source Packages for BioC 3.14	Source Archive