Test Changes in the Co-Localisation of Cell Types Between Groups of Patients

Documentation for package ‘spicyR’ version 1.99.31

bind	The per-image values of every pair, as a data frame
buildKnnGraph	Build a k-nearest-neighbour graph between cells
colTest	Perform a simple wilcoxon-rank-sum test or t-test on the columns of a data frame
convPairs	Converts colPairs object into an abundance matrix based on number of nearby interactions for every cell type.
diabetesData	Imaging mass cytometry of human pancreas in type 1 diabetes (Damond et al. 2019)
getPairwise	Get statistic from pairwise L curve of a single image.
getPairwiseProp	Observed/expected proportion ratio for a fixed-k neighbourhood
getProp	Get proportions from a SummarizedExperiment.
imageCrossPlot	Pairwise cross-plot of spatial associations
plotImage	Plot one image, showing the 'from' and 'to' cells of a pair
signifPlot	Plots result of signifPlot.
spicy	Test for changes in the co-localisation of cell types between conditions
spicyBoxPlot	Box plot of one pair, with a point per image
SpicyResults	The results of spicy()
SpicyResults-class	The results of spicy()
spicyTest	Results of the image-level test on diabetesData
topPairs	A table of the significant results from spicy tests
topPairs-method	A table of the significant results from spicy tests
writeCellStore	Write cells as a SpatialData Zarr store