# Spatial analysis of in situ cytometry data

## Documentation for package ‘spicyR’ version 0.99.13

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

## Help Pages

Accessors | 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
filterCells | Accessors for SegmentedCells
filterCells-method | Accessors for SegmentedCells
geom_hatching | hatchingPlot
getPairwise | Get statistic from pairwise L curve of a single image.
hatchingPlot | hatchingPlot
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
lisa | Generate local indicators of spatial association
melanomaResponders | Melanoma responders/non-responders dataset.
plot | A basic plot for SegmentedCells object
plot-SegmentedCells | A basic plot for SegmentedCells object
region | Accessors for SegmentedCells
region-method | Accessors for SegmentedCells
region<- | Accessors for SegmentedCells
region<--method | Accessors for SegmentedCells
scale_region | Scale constructor for regions
scale_region_manual | Scale constructor for regions
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 melanomaResponders data
spicyTestBootstrap | Results from spicy with bootstrap for melanomaResponders data
topPairs | A table of the significant results from spicy tests
topPairs-method | A table of the significant results from spicy tests