Package: sbivar 0.99.37

Stijn Hawinkel

sbivar: Test for Spatial Bivariate Association Across Omics Types

Sbivar implements a suite of tests for Spatial BIVARiate association across omics modalities, with possibly disjoint coordinate sets. Implemented tests are generalized additive models (GAMs), modified t-test, bivariate Moran's I and Gaussian processes (GPs). Both single images and replicated experiments can be analysed.

Authors:Stijn Hawinkel [cre, aut], Wangjun Hu [aut]

sbivar_0.99.37.tar.gz
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sbivar_0.99.37.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
sbivar/json (API)

# Install 'sbivar' in R:

install.packages('sbivar', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sthawinke/sbivar/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

Vicari - Spatial transcriptomics and metabolomics data of mouse brain

On CRAN:

transcriptomics spatial proteomics metabolomics openblas cpp

4.18 score 4 scripts 17 exports 132 dependencies

Last updated from:ddcce07ff3. Checks:14 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	209
linux-devel-arm64	NOTE	333
linux-devel-x86_64	NOTE	456
source / vignettes	OK	429
linux-release-arm64	NOTE	359
linux-release-x86_64	NOTE	463
macos-release-arm64	NOTE	401
macos-release-x86_64	NOTE	574
macos-oldrel-arm64	NOTE	458
macos-oldrel-x86_64	NOTE	421
windows-devel-arm64	NOTE	2073
windows-devel-x86_64	NOTE	2631
windows-release-arm64	NOTE	1901
windows-release-x86_64	NOTE	2580
windows-oldrel-x86_64	NOTE	2583
wasm-release	OK	210

Exports:buildNewGrid exploreWeights extractResultsMulti fitLinModels normMat plotCoords plotCoordsMulti plotGAMs plotGAMsTopPair plotPairMulti plotPairSingle plotSpotSums plotTopPair sbivar selfName topPairs writeSbivarToXlsx

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocParallel bit bit64 blob boot cachem class classInt cli codetools concaveman cpp11 curl DBI dbplyr DelayedArray deldir dplyr e1071 farver fastmap fastmatrix filelock FNN formatR futile.logger futile.options generics GenomicRanges ggplot2 glue goftest gstat gtable httr2 intervals IRanges isoband jsonlite KernSmooth labeling lambda.r lattice lifecycle lme4 lmerTest magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv minqa MultiAssayExperiment nlme nloptr numDeriv openssl openxlsx pillar pkgconfig polyclip proxy purrr R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel Rdpack reformulas Rfast rjson rlang rpart RSQLite s2 S4Arrays S4Vectors S7 scales Seqinfo sf sftime SingleCellExperiment smoppix snow sp spacetime SparseArray SpatialExperiment SpatialPack spatstat.data spatstat.explore spatstat.geom spatstat.model spatstat.random spatstat.sparse spatstat.univar spatstat.utils stars stringi stringr SummarizedExperiment sys tensor tibble tidyr tidyselect units utf8 V8 vctrs viridisLite withr wk xts XVector zigg zip zoo

Vignette of the sbivar package

Rendered fromsbivarVignette.Rmdusingknitr::rmarkdown

Last update: 2026-09-14
Started: 2025-08-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add columns with feature names to a matrix by splitting rownames, and remove rownames	addFeatureColumn
Construct the nxnxg/2 array of derivatives for a nxn matrix to the g/2 covariance matrix parameters.	arrayDeriv
Multiply an array with a matrix	arrayMatProd
Find traces of all inner products of matrices composing arrays A and B yielding a pxp matrix	arrayProd2tr
Find traces of all inner products of matrices composing arrays A and B, after transposing the second yielding a pxp matrix	arrayProdTr
Extract an assay, and transpose	assayT
A wrapper for Matrix::bdiag maintaining names	bdiagn
Construct cross-blocks of alternative covariance matrices at different length scales	buildAltSigmas
Build a 3-slice array of covariance-parameter derivatives	buildDerivArray
Build a new grid covering the convex hull around two coordinate matrices	buildNewGrid
Build the SAC matrix for a Gaussian process	buildSigmaGp
Build a weight matrix for bivariate Moran's I	buildWeightMat
An analytical p-value combination method using the Cauchy distribution.	CCT
Check input of matrices and lists	checkInputSingle
Find all cross-correlations for a list of matrices	correlationsMulti
Evaluate a variogram on a set of distances	evalVariogram
Visualize different weighting functions	exploreWeights
Is there any double underscore in the character vector?	findDoubleUnderScore
Fit a GAM model to a single variable	fitGAM
Fit a Gaussian process (GP) to a single outcome vector	fitGP
Fit a linear model for an individual feature pair	fitLinModel
Fit linear models on result@result calculated for replicated images, and extract the results	extractResultsMulti fitLinModels
Fit GAMs to all columns of a dataframe, as a wrapper for fitGAM	fitManyGAMs
A wrapper to fit GPs on all columns of a matrix	fitManyGPs
Fit GAMs and find correlations and standard error for data lists	GAMsMulti
Fit univariate GAMs and test bivariate combinations	GAMsSingle
Construct the SAC part of the covariance matrix using the Gaussian covariance kernel,	GaussKernel
Approximate variance of the spatial covariance numerator	getApproxVar
Get all categrocial variables from a dataframe	getDiscreteVars
Return feature names from a list	getFeaturesList
Construct the size variable	getSize
Extract coordinate matrix	getSpatialCoords
Extract data matrix	getX
Fit Gaussian processes (GPs) if needed, and perform score tests	GPsSingle
Make unique names	makeNames
Make a list of offsets	makeOffset
Convert z-value to p-value	makePval
Estimate variograms using Matheron's binning estimator for many features at once, and evaluate	matheronVariograms
Perform modified t-tests for all pairs	ModTtestSingle
Find all Moran's I statistics for a list of matrices	MoransIMulti
Calculate bivariate Moran's I between two modality matrix, with variance and p-value	MoransISingle
Move two sets of coordinates to 0-1. without shifting them with respect to each other	moveTwoCoords
Normalize a data matrix, and ensure correct column names	normMat
Plot the coordinates of two omics modalities	plotCoords plotCoordsMulti
Plot the fitted splines, and the correlation between them	plotGAMs
Plot GAMs of top features	plotGAMsTopPair plotGAMsTopPair,sbivarResultsGAMs-method
Plot a specified feature pair for the data provided	plotPairMulti plotPairSingle plotPairSingleVectors
Plot the spot-wise sums of the two modalities across the slices	plotSpotSums
Plot a the top feature pair according to a sbivar analysis	plotTopPair plotTopPair,sbivarResults-method
Print a message for the current iteration	printIteration
Print feature progress	printProgress
Replace the left hand side of a formula by a fixed string	replaceLhs
Spatial bivariate association analysis	sbivar sbivar,list,list-method sbivar,matrix,matrix-method sbivar,MultiAssayExperiment,ANY-method sbivar,SpatialExperiment,SpatialExperiment-method
Estimate measures of bivariate spatial association for multiple images	sbivarMulti
Test for bivariate spatial association in a single image	sbivarSingle
Wrapper to normalize, select feature and scale	scaleHelpFun
Scale to [-1,1] range	scaleMinusOne
Scale to [0,1] range	scaleZeroOne
Name a character vector after itself	selfName
Split a SpatialExperiment object into images	splitSpatialExperiment
Split a string	sund
Test for correlation between the predictions of two GAM models	testGAM
Perform a score test on the bivariate spatial association in a Gaussian process.	testGP
Return the top results found by sbivar	topPairs topPairs,sbivarResults-method
Find trace of a matrix, of traces of an array	tr
Return predictions of a GAM, along with the factored coefficient covariance	vcovPredGam
Spatial transcriptomics and metabolomics data of mouse brain	Vicari
Write _sbivar_ results to an excel worksheet	writeSbivarToXlsx writeSbivarToXlsx,sbivarResults-method