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

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Documentation for package ‘sosta’ version 0.99.5

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