Package: sosta 0.99.5

Samuel Gunz

sosta: A package for the analysis of anatomical tissue structures in spatial omics data

sosta (Spatial Omics STructure Analysis) is a package for analyzing spatial omics data to explore tissue organization at the anatomical structure level. It reconstructs morphologically relevant structures based on molecular features or cell types. It further calculates a range of structural and shape metrics to quantitatively describe tissue architecture. The package is designed to integrate with other packages for the analysis of spatial (omics) data.

Authors:Samuel Gunz [aut, cre], Mark D. Robinson [aut, fnd]

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sosta_0.99.5.tgz(r-4.4-emscripten)
sosta.pdf |sosta.html✨
sosta/json (API)
NEWS

# Install 'sosta' in R:

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

Bug tracker:https://github.com/sgunz/sosta/issues

Pkgdown site:https://sgunz.github.io

Datasets:

sostaSPE - Example SpatialExperiment Object with Simulated Tissue Images and Point Patterns

On BioConductor:sosta-0.99.4(bioc 3.21)

software spatial transcriptomics visualization

5.68 score 1 stars 1 packages 2 scripts 111 downloads 23 exports 125 dependencies

Last updated 4 days agofrom:3e9e98c29b. Checks:7 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 22 2025
R-4.5-win	OK	Mar 22 2025
R-4.5-mac	OK	Mar 22 2025
R-4.5-linux	OK	Mar 22 2025
R-4.4-win	OK	Mar 22 2025
R-4.4-mac	OK	Mar 22 2025
R-4.4-linux	OK	Mar 22 2025

Exports:assingCellsToStructures binaryImageToSF cellTypeProportions createPointPatternTissue estimateReconstructionParametersSPE findIntensityThreshold getDimXY meanShapeMetrics minBoundaryDistances normalizeCoordinates reconstructShapeDensity reconstructShapeDensityImage reconstructShapeDensitySPE shapeIntensityImage shapeMetrics simulateTissueBlobs spatialCoords2SF SPE2ppp stCalculateCurvature stCalculateShapeCurl stFeatureAxes totalShapeMetrics xyCoordinates

Dependencies:abind askpass base64enc Biobase BiocFileCache BiocGenerics bit bit64 bitops blob bslib cachem class classInt cli colorspace cpp11 crayon curl DBI dbplyr DelayedArray deldir digest dplyr e1071 EBImage evaluate fansi farver fastmap fftwtools filelock fontawesome fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue goftest gtable highr htmltools htmlwidgets httr IRanges isoband jpeg jquerylib jsonlite KernSmooth knitr labeling lattice lifecycle locfit magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl patchwork pillar pkgconfig plogr png polyclip proxy purrr R6 rappdirs RColorBrewer Rcpp RCurl rjson rlang rmarkdown RSQLite s2 S4Arrays S4Vectors sass scales sf SingleCellExperiment smoothr SparseArray SpatialExperiment spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr SummarizedExperiment sys tensor terra tibble tidyr tidyselect tiff tinytex UCSC.utils units utf8 vctrs viridisLite withr wk xfun XVector yaml

Overview of sosta

Samuel Gunz, Mark D. Robinson

Rendered fromStructureReconstructionVignette.Rmdusingknitr::rmarkdownon Mar 22 2025.

Last update: 2025-03-21
Started: 2025-03-21

Reconstruction and analysis of pancreatic islets from IMC data

Samuel Gunz, Mark D. Robinson

Rendered fromImcDiabetesIsletsVignette.Rmdusingknitr::rmarkdownon Mar 22 2025.

Last update: 2025-03-21
Started: 2025-03-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Function to estimate the intensity image of a point pattern	.intensityImage
Function to estimate the intensity threshold for the reconstruction of spatial structures	.intensityThreshold
Function to assign spatial points to structures	assingCellsToStructures
Converts a binary matrix to an sf polygon	binaryImageToSF
Calculate the proportion of each cell type within spatial structures	cellTypeProportions
Create a Point Pattern on a Simulated Tissue Image	createPointPatternTissue
Estimate reconstruction parameters from a set of images	estimateReconstructionParametersSPE
Estimate the intensity threshold for the reconstruction of spatial structures	findIntensityThreshold
Function to get the dimension based on dim of y axis	getDimXY
Calculate mean shape metrics of a set of polygons	meanShapeMetrics
Compute minimum boundary distances for each cell within its corresponding image structures	minBoundaryDistances
Function to normalize coordinates between zero and one while keep scaling	normalizeCoordinates
Reconstruct polygon from point pattern density	reconstructShapeDensity
Reconstruct structure from spe object with given image id	reconstructShapeDensityImage
Reconstruct structure from spatial experiment object per image id	reconstructShapeDensitySPE
Intensity plot	shapeIntensityImage
Calculate a set of shape metrics of a polygon	shapeMetrics
Simulate Tissue Blobs	simulateTissueBlobs
Example SpatialExperiment Object with Simulated Tissue Images and Point Patterns	sostaSPE
Function to convert spatialCoords to an sf object	spatialCoords2SF
Function to convert spatial coordinates of a 'SpatialExperiment' object to a 'ppp' object	SPE2ppp
Calculate curvature of sf object	stCalculateCurvature
Calculate curl of a polygon	stCalculateShapeCurl
Calculate the length of feature axes of an sf polygon	stFeatureAxes
Calculate a set of shape metrics of a set of polygons	totalShapeMetrics
Function to extract x y coordinates from binary image	xyCoordinates