Package index

Test

Every pair of cell types, between conditions or with survival.

spicy()

Test for changes in the co-localisation of cell types between conditions

SpicyResults-class SpicyResults

The results of spicy()

topPairs()

A table of the significant results from spicy tests

bind()

The per-image values of every pair, as a data frame

Plot

signifPlot()

Plots result of signifPlot.

spicyBoxPlot()

Box plot of one pair, with a point per image

plotImage()

Plot one image, showing the from and to cells of a pair

imageCrossPlot()

Pairwise cross-plot of spatial associations

Per-image statistics (image method)

Inputs and helpers for spicy(method = "image"), the original spicyR test.

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.

buildKnnGraph()

Build a k-nearest-neighbour graph between cells

convPairs()

Converts colPairs object into an abundance matrix based on number of nearby interactions for every cell type.

colTest()

Perform a simple wilcoxon-rank-sum test or t-test on the columns of a data frame

Large data sets

Cells stored on disk as a SpatialData Zarr store, which spicy() reads image by image.

writeCellStore()

Write cells as a SpatialData Zarr store

Data

diabetesData

Imaging mass cytometry of human pancreas in type 1 diabetes (Damond et al. 2019)

spicyTest

Results of the image-level test on diabetesData