CellexalVR can color graphs based on different attribute types, such as cell types. The "Color by attribute" can be pressed to open a menu to color by attribute. The attributes are seperated into different categories which can be seen on top of the menu. Pressing one of the little boxes with a category name will show you the available attributes of that category. The attributes are defined in the meta.cell file. In the top right of the menu, there is a button that says "Switch mode". Pressing this button switches all the buttons between single attribute mode and boolean logic mode.

When in the single attribute mode, press a square to color according to that attribute. Cells not part of that attribute will not be recolored. Pressing multiple buttons in sequence allows you to view the cells that belong to all those attributes simultaneously.

In boolean logic mode, more advanced ways of coloring are allowed. You can choose some attributes that cells must be part of and some attributes that cells must not be part of. The buttons representing the attributes will initially all be black, which means that they are not considered when evaluating the coloring, pressing one of the attributes switches it to green which means that cells must be part of that attribute, pressing the attribute once more switches the color to red and means that cells must not be part of that attribute. All graphs will be recolored every time you change the attributes' states.

On the top of the menu there is also a button with a plus sign. This button will create a subgraph, read more here.
CellexalVR also features what we call over the top coloring which allows you to use even more complicated boolean logic expressions to color graphs. This requires you to type your logic into a text file that will be loaded into CellexalVR. You can read more about the format of this text file in the file format section. If any of these files are present in the dataset, a tab will appear at the top of the menu that says "Boolean expressions". Click the box underneath this text to switch to that tab and then click a square to color all graphs based on that boolean expression.

After you color graphs based on an attribute, you can view information about the currently colored attributes in the legend.