ggspavis

The ggspavis package contains visualization functions for spatial transcriptomics data, including 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 Bioconductor format.

The package is available from Bioconductor.

Installation

The release version of the package can be installed from Bioconductor:

install.packages("BiocManager")
BiocManager::install("ggspavis")

The latest development version can be installed either from the development version of Bioconductor or from GitHub:

remotes::install_github("lmweber/ggspavis")

Tutorial

A vignette containing a tutorial and examples is available from the Bioconductor package page.

Citation

• Righell D.*, Weber L.M.*, Crowell H.L.*, Pardo B., Collado-Torres L., Ghazanfar S., Lun A.T.L., Hicks S.C.*, and Risso D.* (2022). SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor. Bioinformatics, btac299.