Registration Open for Bioc2024
Early registration discount pricing ends May 31!


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

Visualization functions for spatial transcriptomics data

Bioconductor version: Development (3.20)

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>

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


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

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

ggspavis overview HTML R Script
Reference Manual PDF


biocViews DimensionReduction, GeneExpression, QualityControl, SingleCell, Software, Spatial, Transcriptomics
Version 1.11.0
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
Bug Reports
See More
Suggests BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix, scater, scran, uwot, testthat, patchwork
Linking To
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_1.11.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) ggspavis_1.11.0.tgz
macOS Binary (arm64) ggspavis_1.11.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats