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ggspavis

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

Visualization functions for spatial transcriptomics data


Bioconductor version: Development (3.19)

Visualization functions for spatial transcriptomics data. Includes functions to generate several types of plots, including spot plots, feature (molecule) plots, reduced dimension plots, spot-level quality control (QC) plots, and feature-level QC plots, for datasets from the 10x Genomics Visium and other technological platforms. Datasets are assumed to be in either SpatialExperiment or SingleCellExperiment format.

Author: Lukas M. Weber [aut, cre] , Helena L. Crowell [aut] , Yixing E. Dong [aut]

Maintainer: Lukas M. Weber <lmweberedu at gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ggspavis")

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("ggspavis")
ggspavis overview HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DimensionReduction, GeneExpression, QualityControl, SingleCell, Software, Spatial, Transcriptomics
Version 1.9.5
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License MIT + file LICENSE
Depends ggplot2
Imports SpatialExperiment, SingleCellExperiment, SummarizedExperiment, ggside, grid, ggrepel, RColorBrewer, scales, grDevices, methods, stats
System Requirements
URL https://github.com/lmweber/ggspavis
Bug Reports https://github.com/lmweber/ggspavis/issues
See More
Suggests BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix, scater, scran, uwot, testthat, patchwork
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me Banksy, HCATonsilData
Links To Me
Build Report Build Report

Package Archives

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

Source Package ggspavis_1.9.5.tar.gz
Windows Binary ggspavis_1.9.5.zip
macOS Binary (x86_64) ggspavis_1.9.5.tgz
macOS Binary (arm64) ggspavis_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ggspavis
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ggspavis
Bioc Package Browser https://code.bioconductor.org/browse/ggspavis/
Package Short Url https://bioconductor.org/packages/ggspavis/
Package Downloads Report Download Stats