ggspavis

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see ggspavis.

Visualization functions for spatial transcriptomics data

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0002-3282-1730 , Helena L. Crowell [aut] ORCID iD ORCID: 0000-0002-4801-1767 , Yixing E. Dong [aut] ORCID iD ORCID: 0009-0003-5115-5686

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

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

Installation

To install this package, start R (version "4.5") and enter:


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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DimensionReduction, GeneExpression, QualityControl, SingleCell, Software, Spatial, Transcriptomics

Version 1.14.3

In Bioconductor since BioC 3.14 (R-4.1) (4 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

Suggests BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix, scater, scran, uwot, testthat, patchwork

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me smoothclust, HCATonsilData

Links To Me

Build Report Build Report

Package Archives

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

Source Package ggspavis_1.14.3.tar.gz

Windows Binary (x86_64) ggspavis_1.14.3.zip

macOS Binary (x86_64) ggspavis_1.14.3.tgz

macOS Binary (arm64) ggspavis_1.14.3.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

Old Source Packages for BioC 3.21 Source Archive