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

## Documentation for package ‘sosta’ version 1.3.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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
minCellTypeStructDist | Compute minimum distances from each cell types to structure boundaries per structure
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