A common analysis task for single-cell chromatin data is genome browser-style data visualization for different groups of cells. Signac enables such visualizations with cells dynamically grouped into different pseudo-bulk tracks by reading Tn5 integration data from a position-indexed fragment file44. To visualize pseudo-bulk accessibility tracks for different groups of cells, we constructed a sparse matrix of base-resolution Tn5 integration events, where each row was a cell and each column a DNA base in the requested region. We then grouped cells and computed the total accessibility at each site within each group and scaled the total accessibility within each group by the total number of cells in the group and the average total counts for cells in each group to account for differences in overall chromatin signal and cell number between different groups of cells. We then smoothed the chromatin signal across small regions by computing a rolling window sum across the genomic region for each group of cells (using a window size of 100 bp by default). This was implemented in the CoveragePlot function in Signac. We also implemented an
