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:Lambda Moses [aut, cre], Alik Huseynov [aut], Kayla Jackson [aut], Laura Luebbert [aut], Lior Pachter [aut, rev]

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)
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Voyager_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Voyager/json (API)

# 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

Datasets:

ditto_colors - Colorblind friendly palette from dittoSeq

On BioConductor:Voyager-1.15.0(bioc 3.24)Voyager-1.14.0(bioc 3.23)

geneexpression spatial transcriptomics visualization bioconductor eda esda exploratory-data-analysis omics spatial-statistics spatial-transcriptomics

8.89 score 103 stars 468 scripts 536 downloads 55 exports 168 dependencies

Last updated from:81c6dc0962. Checks:5 WARNING, 2 OK, 3 ERROR. Indexed: yes.

Target	Result	Time
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:annotGeometryMoransI annotGeometryUnivariate args_not_check calculateBivariate calculateMoransI calculateMultivariate calculateUnivariate clusterCorrelograms clusterMoranPlot clusterVariograms colDataMoransI colDataUnivariate colGeometryMoransI colGeometryUnivariate ElbowPlot fun getDivergeRange info is_joint is_local listSFEMethods moranBounds moranPlot multispati_rsp plotAnnotGraph plotBivariate plotCellBin2D plotColDataFreqpoly plotColDataHistogram plotColGraph plotCorrelogram plotCrossVariogram plotCrossVariogramMap plotDimLoadings plotGeometry plotImage plotLocalResult plotMoranMC plotRowDataFreqpoly plotRowDataHistogram plotSpatialFeature plotTxBin2D plotVariogram plotVariogramMap reducedDimMoransI reducedDimUnivariate reorganize_fun runBivariate runMoransI runMultivariate runUnivariate SFEMethod spatialReducedDim use_graph use_matrix

Dependencies:abind askpass assorthead backports base64enc beachmat BH Biobase BiocFileCache BiocGenerics biocmake BiocNeighbors BiocParallel bit bit64 bitops blob bluster boot bslib cachem checkmate class classInt cli cluster coda codetools cpp11 curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deldir digest dir.expiry dplyr dqrng DropletUtils e1071 EBImage edgeR evaluate farver fastmap fftwtools filelock fontawesome formatR Formula fs futile.logger futile.options generics GenomicRanges geometries ggnewscale ggplot2 glue gtable h5mread HDF5Array highr htmltools htmlwidgets httr2 igraph insight IRanges isoband jpeg jquerylib jsonlite KernSmooth knitr labeling lambda.r lattice LearnBayes lifecycle limma locfit magick magrittr marginaleffects MASS Matrix MatrixGenerics matrixStats memoise memuse mime multcomp mvtnorm nlme openssl patchwork pillar pkgconfig png proxy purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown RSpectra RSQLite s2 S4Arrays S4Vectors S7 sandwich sass scales scico scuttle Seqinfo sf sfheaders SingleCellExperiment sitmo snow sp SparseArray sparseMatrixStats SpatialExperiment SpatialFeatureExperiment spatialreg spData spdep statmod stringi stringr SummarizedExperiment survival sys terra TH.data tibble tidyr tidyselect tiff tinytex units utf8 vctrs viridisLite withr wk xfun XVector yaml zeallot zoo

Overview of Voyager

Rendered fromoverview.Rmdusingknitr::rmarkdown

Last update: 2024-04-29
Started: 2022-07-07

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

Package: Voyager 1.15.0

Voyager: From geospatial to spatial omics

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