Package: ggspavis 1.19.0

Lukas M. Weber

ggspavis: Visualization functions for spatial transcriptomics data

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.

Authors:Lukas M. Weber [aut, cre], Helena L. Crowell [aut], Yixing E. Dong [aut]

ggspavis_1.19.0.tar.gz
ggspavis_1.19.0.zip(r-4.7)ggspavis_1.19.0.zip(r-4.6)ggspavis_1.19.0.zip(r-4.5)
ggspavis_1.19.0.tgz(r-4.6-any)ggspavis_1.19.0.tgz(r-4.5-any)
ggspavis_1.19.0.tar.gz(r-4.7-any)ggspavis_1.19.0.tar.gz(r-4.6-any)
ggspavis_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ggspavis/json (API)
NEWS

# Install 'ggspavis' in R:
install.packages('ggspavis', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lmweber/ggspavis/issues

On BioConductor:ggspavis-1.19.0(bioc 3.24)ggspavis-1.18.0(bioc 3.23)

spatialsinglecelltranscriptomicsgeneexpressionqualitycontroldimensionreduction

7.19 score 5 stars 514 scripts 642 downloads 9 exports 69 dependencies

Last updated from:7872157823. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE250
linux-devel-x86_64WARNING427
source / vignettesOK613
linux-release-x86_64WARNING586
macos-release-arm64WARNING268
macos-oldrel-arm64WARNING237
windows-develWARNING470
windows-releaseWARNING415
windows-oldrelWARNING542
wasm-releaseOK238

Exports:plotCoordsplotDimRedplotFeatureQCplotMoleculesplotObsQCplotQCplotSpotQCplotSpotsplotVisium

Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11curlDBIdbplyrDelayedArraydplyrfarverfastmapfilelockgenericsGenomicRangesggplot2ggrepelggsidegluegtablehttr2IRangesisobandlabelinglatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigpurrrR6rappdirsRColorBrewerRcpprjsonrlangRSQLiteS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrsviridisLitewithrXVector

ggspavis overview

Lukas M. Weber, Helena L. Crowell, Yixing E. Dong

Rendered fromggspavis_overview.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-10-06
Started: 2020-12-14

Readme and manuals

Help Manual

Help pageTopics
plotCoordsplotCoords plotSpots
plotDimRedplotDimRed
plotFeatureQCplotFeatureQC
plotMoleculesplotMolecules
plotObsQCplotObsQC plotQC plotSpotQC
plotVisiumplotVisium