Introduction | Examples | Sequencing-based spatial transcriptomics data | Spot shape - Slide-seq and Visium | Quality control (QC) plots | Spot/bin/cell-level QC | Feature-level QC | Bin shape - Visium HD | Imaging-based spatial transcriptomics data | Reduced dimension plots | Session information
Package: ggspavis 1.18.1
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:
ggspavis_1.18.1.tar.gz
ggspavis_1.18.1.zip(r-4.7-any)ggspavis_1.18.1.zip(r-4.6-any)ggspavis_1.18.1.zip(r-4.5-any)
ggspavis_1.18.1.tgz(r-4.6-any)ggspavis_1.18.1.tgz(r-4.5-any)
ggspavis_1.18.1.tar.gz(r-4.7-any)ggspavis_1.18.1.tar.gz(r-4.6-any)
ggspavis_1.18.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ggspavis/json (API)
| # Install 'ggspavis' in R: |
| install.packages('ggspavis', repos = c('https://bioc-release.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
Last updated from:37e2c4a62d (on RELEASE_3_23). Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 297 | ||
| linux-devel-x86_64 | WARNING | 964 | ||
| source / vignettes | OK | 1425 | ||
| linux-release-x86_64 | WARNING | 468 | ||
| macos-release-arm64 | WARNING | 575 | ||
| macos-oldrel-arm64 | WARNING | 804 | ||
| windows-devel | WARNING | 477 | ||
| windows-release | WARNING | 542 | ||
| windows-oldrel | WARNING | 430 | ||
| wasm-release | OK | 216 |
Exports:plotCoordsplotDimRedplotFeatureQCplotMoleculesplotObsQCplotQCplotSpotQCplotSpotsplotVisium
Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11curlDBIdbplyrDelayedArraydplyrfarverfastmapfilelockgenericsGenomicRangesggplot2ggrepelggsidegluegtablehttr2IRangesisobandlabelinglatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigpurrrR6RColorBrewerRcpprjsonrlangRSQLiteS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| plotCoords | plotCoords plotSpots |
| plotDimRed | plotDimRed |
| plotFeatureQC | plotFeatureQC |
| plotMolecules | plotMolecules |
| plotObsQC | plotObsQC plotQC plotSpotQC |
| plotVisium | plotVisium |
