ggcyto
Visualize Cytometry data with ggplot
Bioconductor version: Release (3.20)
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 "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, FlowCytometry, ImmunoOncology, Infrastructure, Software, Visualization |
| Version | 1.34.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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 |
| System Requirements | |
| URL | https://github.com/RGLab/ggcyto/issues |
See More
| Suggests | testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr |
| Linking To | |
| Enhances | |
| Depends On Me | flowGate |
| Imports Me | CytoML, CytoPipeline |
| 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_1.34.0.tar.gz |
| Windows Binary (x86_64) | ggcyto_1.34.0.zip |
| macOS Binary (x86_64) | ggcyto_1.34.0.tgz |
| macOS Binary (arm64) | ggcyto_1.33.0.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 |