Correlation Heatmap of distal elements and promoters between clusters

[abbaslab]

In Corces et al (Science 2018), Figure 2A has an informative correlation heatmap across the different cancer types separately for the distal elements, promoters and transcripts across the TCGA bulk ATAC seq analysis.

Is there a function in ArchR or a way to output data to be then used for input into a correlation heatmap to generate the correlation between the scATAC clusters with respect to Distal elements (as defined by ArchR?), promoters and gene activity separately, like what was done in Corces et al paper?

(reference Corces et al Science 2018)

[rcorces]

These heatmaps are from bulk data. You would not make such a heatmap from single cells. You can make pseudobulks from your scATAC clusters and then use getGroupSE() to get a SummarizedExperiment https://www.archrproject.com/reference/getGroupSE.html