How SCP renders data in scatter plots

Single Cell Portal has special logic depending on the type of scatter plot to address issues surrounding over-plotting.

Group-based annotations

Any scatter plot that is displaying group-based annotations (categorical labels) is ordered based on the number of cells per label.  The largest group is plotted first, followed by the second largest, and so on.  This ensures that smaller populations have less chance of being hidden by a larger group.  Any group can be brought to the front of a scatter plot by hovering over that label in the legend.

Expression-based plots

Since identifying groups of cells by their expression signatures is a vital analytical tool, having populations obscured by other ones can be misleading or provide an incomplete picture.  To help address this, cells in expression-based scatter plots are sorted by their expression value.  The order can be controlled by using the "Order expression by" dropdown menu in the Options panel on the righthand side of the page.  There are three supported options:

High

By default, cells with the highest expression cells are plotted on top in descending order.

Low

Sometimes, you want to see cells that are expressing a gene least, while still expressing it.  Using the "low" option can can enable you to distinguish such cell populations that cluster closely with highly-expressing cells.  This inverts the order and brings the lowest observed expression values to the front, except cells with no observed expression which are plotted behind all other cells. 

Unsorted

This disables any sorting of cells and instead renders elements in the order in which they appeared in the associated clustering file.  This also prevents moving cells with no observed expression into the background.  This can help you show your data in SCP like you show it in your publication or other analysis output.