Code used to produce the final figures and tables of the study "Spatial Transcriptomics in Breast Cancer Reveals Tumour Microenvironment-Driven Drug Responses and Clonal Therapeutic Heterogeneity".

Use the git clone command to create a local copy:

git clone https://github.com/cnio-bu/breast-bcspatial

You need to download additional data folders from Zenodo (DOI: 10.5281/zenodo.10638906) for the code to be functional:

• visium/: Contains processed spatial transcriptomics Seurat objects with deconvoluted spots, SCTransform-normalised counts, and clonal composition predicted with SCEVAN [1]. Please make sure to merge the contents of this folder with the data/visium/scalefactors folder that is provided in this repository.

• single-cell/: Contains raw and filtered merged single-cell RNA-seq Seurat objects with unnormalised counts used as a reference for spot deconvolution.

• beyondcell/sensitivity: Contains Beyondcell sensitivity objects with prediction scores for all drug response signatures in SSc breast.

• beyondcell/functional: Contains Beyondcell functional objects with enrichment scores for all functional signatures.

These objects were generated with the code available at cnio-bu/ST-preprocess.

References

1. De Falco A, Caruso F, Su X-D, Iavarone A, Ceccarelli M. A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data. Nat Commun. 2023;14:1074.

Once all data is downloaded, just run the code in the scripts/ folder in order. Then, run the code in the scripts/figures_and_tables folder to generate the final figures and tables.

• María José Jiménez-Santos

If you have any questions, feel free to submit an issue.