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

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Documentation for package ‘sosta’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

.df2ppp	Function to convert 'data.frame' to 'ppp' object
.intensityImage	Function to estimate the intensity image of a point pattern
.intensityThreshold	Function to estimate the intensity threshold for the reconstruction of spatial structures
.SPE2df	Function to convert 'SpatialExperiment' object to a data frame
assingCellsToStructures	Function to assign points / coordinates 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