# Spatial analysis of in situ cytometry data

## Documentation for package ‘spicyR’ version 1.12.2

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

## Help Pages

Accessors | Accessors for SegmentedCells
as.data.frame.SegmentedCells | as.data.frame
cellAnnotation | Accessors for SegmentedCells
cellAnnotation-method | Accessors for SegmentedCells
cellAnnotation<- | Accessors for SegmentedCells
cellAnnotation<--method | Accessors for SegmentedCells
cellID | Accessors for SegmentedCells
cellID-method | Accessors for SegmentedCells
cellID<- | Accessors for SegmentedCells
cellID<--method | Accessors for SegmentedCells
cellMarks | Accessors for SegmentedCells
cellMarks-method | Accessors for SegmentedCells
cellMarks<- | Accessors for SegmentedCells
cellMarks<--method | Accessors for SegmentedCells
cellMorph | Accessors for SegmentedCells
cellMorph-method | Accessors for SegmentedCells
cellMorph<- | Accessors for SegmentedCells
cellMorph<--method | Accessors for SegmentedCells
cellSummary | Accessors for SegmentedCells
cellSummary-method | Accessors for SegmentedCells
cellSummary<- | Accessors for SegmentedCells
cellSummary<--method | Accessors for SegmentedCells
cellType | Accessors for SegmentedCells
cellType-method | Accessors for SegmentedCells
cellType<- | Accessors for SegmentedCells
cellType<--method | Accessors for SegmentedCells
colTest | Perform a simple wilcoxon-rank-sum test or t-test on the columns of a data fram
diabetesData | Diabetes IMC data
diabetesData_SCE | Diabetes IMC data in SCE format.
filterCells | Accessors for SegmentedCells
filterCells-method | Accessors for SegmentedCells
getPairwise | Get statistic from pairwise L curve of a single image.
getProp | Get proportions from a SegmentedCells, SingleCellExperiment, SpatialExperiment or data.frame.
imageCellID | Accessors for SegmentedCells
imageCellID-method | Accessors for SegmentedCells
imageCellID<- | Accessors for SegmentedCells
imageCellID<--method | Accessors for SegmentedCells
imageID | Accessors for SegmentedCells
imageID-method | Accessors for SegmentedCells
imagePheno | Accessors for SegmentedCells
imagePheno-method | Accessors for SegmentedCells
imagePheno<- | Accessors for SegmentedCells
imagePheno<--method | Accessors for SegmentedCells
plot | A basic plot for SegmentedCells object
plot,SegmentedCells | A basic plot for SegmentedCells object
plot-method | A basic plot for SegmentedCells object
SegmentedCells | The SegmentedCells class
SegmentedCells-class | The SegmentedCells class
SegmentedCells-method | The SegmentedCells class
show | Show SegmentedCells
show-SegmentedCells | Show SegmentedCells
signifPlot | Plots result of signifPlot.
spicy | Performs spatial tests on spatial cytometry data.
spicy-method | Performs spatial tests on spatial cytometry data.
SpicyResults-class | Performs spatial tests on spatial cytometry data.
SpicyResults-method | Performs spatial tests on spatial cytometry data.
spicyTest | Results from spicy for diabetesData
spicyTestBootstrap | Results from spicy with bootstrap for diabetesData
topPairs | A table of the significant results from spicy tests
topPairs-method | A table of the significant results from spicy tests