15  Spatial co-localization

15.1 Overview

In this chapter, we will show examples of analyses to investigate spatial co-localization of cell types.

For these analyses, we will use a different dataset that provides single-cell spatial resolution, e.g. from the 10x Genomics Xenium platform.

15.2 Load data from previous steps

We start by loading the data object(s) saved after running the analysis steps from the previous chapters. Code to re-run the previous steps is shown in condensed form in Chapter 4.

15.3 Spatial co-localization of cell types within a single sample

We will use the spicyR Bioconductor package (Canete et al. 2022) for the following examples.

Canete, Nicolas P., Sourish S. Iyengar, John T. Ormerod, Heeva Baharlou, Andrew N. Harman, and Ellis Patrick. 2022. “spicyR: Spatial Analysis of in Situ Cytometry Data in R.” Bioinformatics 38: 3099–3105. https://doi.org/10.1093/bioinformatics/btac268.