ggspavis
Visualization functions for spatial transcriptomics data
Bioconductor version: Release (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 gmail.com>
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DimensionReduction, GeneExpression, QualityControl, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.12.0 |
| 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 |
See More
| 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_1.12.0.tar.gz |
| Windows Binary (x86_64) | ggspavis_1.12.0.zip (64-bit only) |
| macOS Binary (x86_64) | ggspavis_1.12.0.tgz |
| macOS Binary (arm64) | ggspavis_1.12.0.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 |