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

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Documentation for package ‘spicyR’ version 1.99.47

• DESCRIPTION file
• User guides, package vignettes and other documentation
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Help Pages

bind	The per-image values of every pair, or of one pair, as a data frame
buildKnnGraph	Build a k-nearest-neighbour graph between cells
calibrationCheck	Check that spicy() is calibrated on your data by shuffling the condition
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
plot.spicyCalibration	Check that spicy() is calibrated on your data by shuffling the condition
plotImage	Plot images, showing their cell types or the 'from' and 'to' cells of a pair
radiusPlot	The evidence for pairs at each radius
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
summary.spicyCalibration	Check that spicy() is calibrated on your data by shuffling the condition
topPairs	The most significant pairs, or the results of chosen pairs
topPairs-method	The most significant pairs, or the results of chosen pairs
writeCellStore	Write cells as a SpatialData Zarr store