multipointR

multipointR is a package to compare the distribution of cells in an image or across multiple images with labelled point process models.

On a single image, a point process model (ppm) can be used to model the spatial distribution of a cell type point pattern as a function of spatial covariates while accounting for natural spacing of cells. The main model class considered in multipointR are inhomogeneous Gibb's point process models.

Across multiple images, users can either compare coefficients from separately fitting multiple univariate ppm models, or fit one joint model across all images with mppm.

multipointR provides an interface between SpatialExperiment and SpatialFeatureExperiment objects and lets users flexibly define their own ppm/mppm models with R's formula interface.

Installation

You can install the stable release version of multipointR from Bioconductor

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("multipointR")

You can install the development version of multipointR from GitHub with:

# install.packages("devtools")
devtools::install_github("mjemons/multipointR")

Disclaimer

This package is still under active development, the content is therefore subject to change.

Parts of this code were optimised and/or generated with claude.ai. Whenever claude.ai made significant contributions to a code chunk I tried my best to acknowledge this as comments in the code.

Contact

In case you have suggestions to multipointR please consider opening an issue to this repository.