ggcyto

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ggcyto.

Visualize Cytometry data with ggplot

Bioconductor version: 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>

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

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")

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

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CellBasedAssays, FlowCytometry, ImmunoOncology, Infrastructure, Software, Visualization

Version 1.22.0

In Bioconductor since BioC 3.3 (R-3.3) (8 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

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

Imports Me CytoML

Suggests Me CATALYST, flowCore, flowStats, flowTime, flowWorkspace, openCyto

Links To Me

Build Report 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

Bioc Package Browser https://code.bioconductor.org/browse/ggcyto/

Package Short Url https://bioconductor.org/packages/ggcyto/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.14 Source Archive