Overview of the SPIAT package

Anna Trigos, Yuzhou Feng, Tianpei Yang, Mabel Li, John Zhu, Volkan Ozcoban, Maria Doyle

19 August 2024

Source: vignettes/SPIAT.Rmd

Introduction

SPIAT (Spatial Image Analysis of Tissues) is an R package with a suite of data processing, quality control, visualisation and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes.

SPIAT includes six analysis modules that allow visualisation, calculation of cell colocalisation, categorisation of the immune microenvironment relative to tumour areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.

An overview of the functions available is shown in the figure below.

You can access the vignettes for other modules of SPIAT here:

Data reading and formatting

Quality control and visualisation

Basic analysis

Cell colocalisation

Spatial heterogeneity

Tissue structure

Cellular neighborhood

Installing SPIAT

SPIAT is a R package available via the Bioconductor repository for packages.

if (!requireNamespace("BiocManager", quietly = TRUE)) {
      install.packages("BiocManager")}
BiocManager::install("SPIAT")

You can also install the latest development version from Github.

if (!requireNamespace("devtools", quietly = TRUE)) {
      install.packages("devtools")}
devtools::install_github("TrigosTeam/SPIAT")

Citing SPIAT

We hope that SPIAT will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!

## Citation info
citation("SPIAT")
#> To cite package 'SPIAT' in publications use:
#> 
#>   Trigos A, Feng Y, Yang T, Li M, Zhu J, Ozcoban V, Doyle M (2024).
#>   _SPIAT: Spatial Image Analysis of Cells in Tissues_. R package
#>   version 1.6.3, <https://trigosteam.github.io/SPIAT/>.
#> 
#>   Feng Y, Yang T, Zhu J, Li M, Doyle M, Ozcoban V, Bass G, Pizzolla A,
#>   Cain L, Weng S, Pasam A, Kocovski N, Huang Y, Keam S, Speed T, Neeson
#>   P, Pearson R, Sandhu S, Goode D, Trigos A (2023). "Spatial analysis
#>   with SPIAT and spaSim to characterize and simulate tissue
#>   microenvironments." _Nature Communications_, *14*(2697).
#>   doi:10.1038/s41467-023-37822-0
#>   <https://doi.org/10.1038/s41467-023-37822-0>.
#> 
#> To see these entries in BibTeX format, use 'print(<citation>,
#> bibtex=TRUE)', 'toBibtex(.)', or set
#> 'options(citation.bibtex.max=999)'.

Author Contributions

AT, YF, TY, ML, JZ, VO, MD are authors of the package code. MD and YF wrote the vignette. AT, YF and TY designed the package.