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ggcyto

Visualize Cytometry data with ggplot

Bioconductor version: Release (3.17)

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")):

Installation

To install this package, start R (version "4.3") 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
LICENSE Text

Details

biocViews CellBasedAssays, FlowCytometry, ImmunoOncology, Infrastructure, Software, Visualization
Version 1.28.1
In Bioconductor since BioC 3.3 (R-3.3) (7.5 years)
License file LICENSE
Depends methods, ggplot2 (>= 3.4.2), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 4.12.1)
Imports plyr, scales, hexbin, data.table, RColorBrewer, gridExtra, rlang
Linking To
Suggests testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr
System Requirements
Enhances
URL https://github.com/RGLab/ggcyto/issues
See More
Depends On Me flowGate
Imports Me CytoML, CytoPipeline
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_1.28.1.tar.gz
Windows Binary ggcyto_1.28.1.zip
macOS Binary (x86_64) ggcyto_1.28.1.tgz
macOS Binary (arm64) ggcyto_1.28.1.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 3.17 Source Archive