ggspavis

Visualization functions for spatial transcriptomics data

Bioconductor version: Release (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")

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	1.10.0
In Bioconductor since	BioC 3.14 (R-4.1) (3 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_1.10.0.tar.gz
Windows Binary (x86_64)	ggspavis_1.10.0.zip
macOS Binary (x86_64)	ggspavis_1.10.0.tgz
macOS Binary (arm64)	ggspavis_1.10.0.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
Old Source Packages for BioC 3.19	Source Archive