Our reference-mapping procedure not only enables the transfer of discrete annotations, but by projecting datasets from multiple modalities into a common space, allows us to explore how variation in one corresponds to variation in another. For example, after integration, we applied diffusion maps to the harmonized measurements to construct a joint differentiation trajectory spanning multiple progenitor states during myeloid differentiation (Fig. 2g). Since this trajectory represents both reference and query cells, we can explore how pseudo-temporal variation in chromatin accessibility correlates with gene expression, even though the two modalities were measured in separate experiments.
