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All functions

Kontextual()
Evaluation of pairwise cell relationships, conditional on a 3rd population.
calcContamination()
Calculate the level of marker contamination of each cell
calcStateChanges()
First layer wrapper function to build linear models measuring state changes
distanceCalculator()
Calculate pairwise distance between cell types
getAbundances()
Wrapper to calculate imhomogenous K function between a cell and surrounding types on each image
getDistances()
Wrapper to calculate pairwise distance between cell types by image
getMarkerMeans()
Extract the average expression for all markers for each cell type in each region defined by lisaClust
isKontextual()
Test whether an object is a kontextualResult
kerenKontextual
Kontextual results from kerenSCE
kerenSCE
MIBI-TOF Breast cancer intensities
kontextCurve()
Evaluation of Kontextual over a range of radii.
kontextPlot()
Plotting the original and kontextual L values over a range of radii.
makeWindow()
Creates a window for a PPP object
parentCombinations()
Create all combinations of cell type relationships from a list of parents
plotStateChanges()
Visualise Cell-Cell Marker Relationships
prepMatrix()
Convert Kontextual or state changes result to a matrix for classification
relabelKontextual() relabel()
Cell permutation for Kontextual