Figure 3 - RegnerM2015/scBreast_scRNA_scATAC_2024 GitHub Wiki

Figure 3 plotting

To further visualize the results from the Basal-like subtype analysis introduced in main Figure 2, we generated a heatmap of effect sizes for significant cancer-specific peak-to-gene associations that involved differentially expressed (upregulated) genes in Basal-like BC cells. We also performed a gene set over-representation/enrichment analysis of the unique genes participating in the heatmap using the clusterProfiler R package.

To zoom in on a specific example of a cancer-specific peak-to-gene association, we visualized the chromatin accessibility landscape of the surrounding locus using ArchR's plotBrowserTrack function and generated dot plots of pseudobulk gene expression in scRNA-seq stratified by condition. Additionally, we visualized the scATAC-seq metacells in a scatter plot of chromatin accessibility at the peak by the inferred level of gene expression.

The Slurm and R scripts below were used to generate these visualizations in the Basal-like subtype analysis:

• scripts/Basal_Cohort_Results-updates-Revised-updated.sh
• scripts/Basal_Cohort_Results-updates-Revised-updated.R