Package index

All functions

SPE2ppp()

Function to convert spatial coordinates of a SpatialExperiment object to a ppp object

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

.SPE2df()

Function to convert SpatialExperiment object to a data frame

.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

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

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