spatialFDA/README.Rmd at devel · mjemons/spatialFDA · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "20%",
  fig.align = 'right'
)
```

# spatialFDA

[![R-CMD-check](https://github.com/mjemons/spatialFDA/actions/workflows/R-CMD-check.yaml/badge.svg?branch=devel)](https://github.com/mjemons/spatialFDA/actions/workflows/R-CMD-check.yaml)

![](inst/extdata/spatialFDA.png){width=20%}

spatialFDA is a tool to calculate spatial statistics functions on a `SpatialExperiment`
object using the `spatstat` library. It contains functions to plot these spatial statistics functions. In addition, users can compare the statial statistics functions using functional data analysis. Here, we use the `refund` library.

## Installation

You can install the official released `Bioconductor` version of `spatialFDA` via

``` r
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("spatialFDA")
```

You can install the development version of `spatialFDA` from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("mjemons/spatialFDA")
```

## Disclaimer

This package is still under active development, the content is therefore subject to change. Please refer to the `Bioconductor` releases for stable versions.

## Contact

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

## Citation

When using `spatialFDA` please cite our pre-print

```
@article {Emons2026.04.13.718197,
	author = {Emons, Martin and Scheipl, Fabian and Gunz, Samuel and Purdom, Elizabeth and Robinson, Mark D},
	title = {Differential co-localisation analysis of multi-sample and multi-condition experiments with spatialFDA},
	year = {2026},
	doi = {10.64898/2026.04.13.718197},
	publisher = {Cold Spring Harbor Laboratory},
	journal = {bioRxiv}
}
```