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 |
getParentPhylo |
Extract parent and all children from a Phylo object |
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. |
Kontextual |
Evaluation of pairwise cell relationships, conditional on a 3rd population. |
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 |
relabel |
Cell permutation for Kontextual |
relabelKontextual |
Cell permutation for Kontextual |