The various types of reduced-dimension plots can be used to identify potentially problematic cells to filter out of the dataset and to interpret cell population structure.
We're past QC now, and marking cells as low-quality just because they don't fit into nice clusters in the expression space seems to be fraught with danger. Why not just focus on what people mostly use these plots for, i.e.:
The various types of reduced-dimension plots can be used to examine the structure of the cell population, including the formation of distinct subpopulations or the presence of continuous trajectories.
We're past QC now, and marking cells as low-quality just because they don't fit into nice clusters in the expression space seems to be fraught with danger. Why not just focus on what people mostly use these plots for, i.e.: