Package: Voyager 1.15.0
Lambda Moses
Voyager: From geospatial to spatial omics
SpatialFeatureExperiment (SFE) is a new S4 class for working with spatial single-cell genomics data. The voyager package implements basic exploratory spatial data analysis (ESDA) methods for SFE. Univariate methods include univariate global spatial ESDA methods such as Moran's I, permutation testing for Moran's I, and correlograms. Bivariate methods include Lee's L and cross variogram. Multivariate methods include MULTISPATI PCA and multivariate local Geary's C recently developed by Anselin. The Voyager package also implements plotting functions to plot SFE data and ESDA results.
Authors:
Voyager_1.15.0.tar.gz
Voyager_1.15.0.zip(r-4.7)Voyager_1.15.0.zip(r-4.6)Voyager_1.15.0.zip(r-4.5)
Voyager_1.15.0.tgz(r-4.6-any)Voyager_1.15.0.tgz(r-4.5-any)
Voyager_1.15.0.tar.gz(r-4.7-any)Voyager_1.15.0.tar.gz(r-4.6-any)
Voyager_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Voyager/json (API)
NEWS
| # Install 'Voyager' in R: |
| install.packages('Voyager', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/pachterlab/voyager/issues
- ditto_colors - Colorblind friendly palette from dittoSeq
On BioConductor:Voyager-1.15.0(bioc 3.24)Voyager-1.14.0(bioc 3.23)
geneexpressionspatialtranscriptomicsvisualizationbioconductoredaesdaexploratory-data-analysisomicsspatial-statisticsspatial-transcriptomics
Last updated from:81c6dc0962. Checks:5 WARNING, 2 OK, 3 ERROR. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 260 | ||
| linux-devel-x86_64 | WARNING | 884 | ||
| source / vignettes | OK | 376 | ||
| linux-release-x86_64 | WARNING | 854 | ||
| macos-release-arm64 | WARNING | 519 | ||
| macos-oldrel-arm64 | WARNING | 542 | ||
| windows-devel | ERROR | 626 | ||
| windows-release | ERROR | 577 | ||
| windows-oldrel | ERROR | 607 | ||
| wasm-release | OK | 233 |
Exports:annotGeometryMoransIannotGeometryUnivariateargs_not_checkcalculateBivariatecalculateMoransIcalculateMultivariatecalculateUnivariateclusterCorrelogramsclusterMoranPlotclusterVariogramscolDataMoransIcolDataUnivariatecolGeometryMoransIcolGeometryUnivariateElbowPlotfungetDivergeRangeinfois_jointis_locallistSFEMethodsmoranBoundsmoranPlotmultispati_rspplotAnnotGraphplotBivariateplotCellBin2DplotColDataFreqpolyplotColDataHistogramplotColGraphplotCorrelogramplotCrossVariogramplotCrossVariogramMapplotDimLoadingsplotGeometryplotImageplotLocalResultplotMoranMCplotRowDataFreqpolyplotRowDataHistogramplotSpatialFeatureplotTxBin2DplotVariogramplotVariogramMapreducedDimMoransIreducedDimUnivariatereorganize_funrunBivariaterunMoransIrunMultivariaterunUnivariateSFEMethodspatialReducedDimuse_graphuse_matrix
Dependencies:abindaskpassassortheadbackportsbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocNeighborsBiocParallelbitbit64bitopsblobblusterbootbslibcachemcheckmateclassclassIntcliclustercodacodetoolscpp11curldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdeldirdigestdir.expirydplyrdqrngDropletUtilse1071EBImageedgeRevaluatefarverfastmapfftwtoolsfilelockfontawesomeformatRFormulafsfutile.loggerfutile.optionsgenericsGenomicRangesgeometriesggnewscaleggplot2gluegtableh5mreadHDF5Arrayhighrhtmltoolshtmlwidgetshttr2igraphinsightIRangesisobandjpegjquerylibjsonliteKernSmoothknitrlabelinglambda.rlatticeLearnBayeslifecyclelimmalocfitmagickmagrittrmarginaleffectsMASSMatrixMatrixGenericsmatrixStatsmemoisememusemimemultcompmvtnormnlmeopensslpatchworkpillarpkgconfigpngproxypurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlrhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSpectraRSQLites2S4ArraysS4VectorsS7sandwichsassscalesscicoscuttleSeqinfosfsfheadersSingleCellExperimentsitmosnowspSparseArraysparseMatrixStatsSpatialExperimentSpatialFeatureExperimentspatialregspDataspdepstatmodstringistringrSummarizedExperimentsurvivalsysterraTH.datatibbletidyrtidyselecttifftinytexunitsutf8vctrsviridisLitewithrwkxfunXVectoryamlzeallotzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Bivariate spatial statistics | calculateBivariate calculateBivariate,ANY-method calculateBivariate,SpatialFeatureExperiment-method runBivariate |
| Multivariate spatial data analysis | calculateMultivariate calculateMultivariate,ANY,character-method calculateMultivariate,ANY,SFEMethod-method calculateMultivariate,SpatialFeatureExperiment,ANY-method runMultivariate |
| Univariate spatial stiatistics | annotGeometryMoransI annotGeometryUnivariate calculateMoransI calculateMoransI,ANY-method calculateMoransI,SpatialFeatureExperiment-method calculateUnivariate calculateUnivariate,ANY,character-method calculateUnivariate,ANY,SFEMethod-method calculateUnivariate,SpatialFeatureExperiment,ANY-method colDataMoransI colDataUnivariate colGeometryMoransI colGeometryUnivariate reducedDimMoransI reducedDimUnivariate runMoransI runUnivariate |
| Find clusters of correlogram patterns | clusterCorrelograms |
| Find clusters on the Moran plot | clusterMoranPlot |
| Cluster variograms of multiple features | clusterVariograms |
| Colorblind friendly palette from dittoSeq | ditto_colors |
| Plot the elbow plot or scree plot for PCA | ElbowPlot |
| Get beginning and end of palette to center a divergent palette | getDivergeRange |
| List all spatial methods in Voyager package | listSFEMethods |
| Compute the bounds of Moran's I given spatial neighborhood graph | moranBounds |
| Use ggplot to plot the moran.plot results | moranPlot |
| A faster implementation of MULTISPATI PCA | multispati_rsp |
| Plot expression of two genes or features with bivariate palette | plotBivariate |
| Plot cell density as 2D histogram | plotCellBin2D |
| Plot frequency polygons for colData and rowData columns | plotColDataFreqpoly plotRowDataFreqpoly |
| Plot histograms for colData and rowData columns | plotColDataHistogram plotRowDataHistogram |
| Plot spatial graphs | plotAnnotGraph plotColGraph |
| Plot correlogram | plotCorrelogram |
| Plot cross variogram | plotCrossVariogram |
| Plot cross variogram map | plotCrossVariogramMap |
| Plot top PC loadings of genes | plotDimLoadings |
| Plot geometries without coloring | plotGeometry |
| Show image without plotting geometries | plotImage |
| Plot local results | plotLocalResult |
| Plot Moran/Geary Monte Carlo results | plotMoranMC |
| Plot gene expression in space | plotSpatialFeature |
| Plot transcript spot density as 2D histogram | plotTxBin2D |
| Plot variogram | plotVariogram |
| Plot variogram maps | plotVariogramMap |
| SFEMethod class | args_not_check args_not_check,SFEMethod-method fun fun,SFEMethod-method info info,SFEMethod-method is_joint is_joint,SFEMethod-method is_local is_local,SFEMethod-method reorganize_fun reorganize_fun,SFEMethod-method SFEMethod SFEMethod-class use_graph use_graph,SFEMethod-method use_matrix use_matrix,SFEMethod-method |
| Plot dimension reduction components in space | spatialReducedDim |
| Compute variograms | .cross_variogram .cross_variogram_map .variogram .variogram_bv .variogram_map variogram-internal |
