# Spatial analysis of in situ cytometry data

## Documentation for package ‘spicyR’ version 1.23.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

bind | Produces a dataframe showing L-function metric for each imageID entry.
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 | Diabetes IMC data in SCE format.
getPairwise | Get statistic from pairwise L curve of a single image.
getProp | Get proportions from a SummarizedExperiment.
imageCrossPlot | Pairwise cross-plot of spatial associations
plotImage | Plots an image with specified from and to cell types.
signifPlot | Plots result of signifPlot.
spicy | Performs spatial tests on spatial cytometry data.
spicy-method | Performs spatial tests on spatial cytometry data.
spicyBoxPlot | Plots boxplot for a specified cell-cell relationship
SpicyResults-class | Performs spatial tests on spatial cytometry data.
SpicyResults-method | Performs spatial tests on spatial cytometry data.
spicyTest | Results from spicy for diabetesData
survBubble | Plots survival results from spicy.
topPairs | A table of the significant results from spicy tests
topPairs-method | A table of the significant results from spicy tests