This repo holds the code for the revised manuscript submitted on 20 Dec 2022.
The data analyses were performed with SPIAT v1.0.4. Data analyses involving (normalised) mixing score calculation were performed with SPIAT v1.0.6. The simulations were performed with spaSim v1.0.2.
To download the versions of SPIAT and spaSim that reproduce the results presented, SPIAT v1.0.4 and spaSim v1.0.2 are available on Bioconductor release 3.16, and SPIAT v1.0.6 is available from https://github.com/TrigosTeam/SPIAT/releases/tag/v1.0.6.
Access the tutorial at: SPIAT vignette and spaSim vignette
The MIBI TNBC dataset was downloaded from: https://www.angelolab.com/mibi-data. The CODEX colon cancer dataset was downloaded from: https://data.mendeley.com/datasets/mpjzbtfgfr/1. The IMC diabetes dataset was downloaded from: https://data.mendeley.com/datasets/cydmwsfztj/1 and https://data.mendeley.com/datasets/cydmwsfztj/2. The prostate cancer and melanoma datasets were generated in-house. Our patient consent does not allow depositing data online.