If you use the “Multiclass” option of Class Marker, you can obtain subgroups in one or more groups of markers as shown in the next figure. The entire class is marked by the A arrow. Inside this group there are three subgroups.

     The B subgroup has a horizontal arrow colored by the color of the class and no other arrow, this means that these markers differentiate this class against all the others.

    The C subgroup has two horizontal arrows, one colored with the color of the current class and another colored gray. This means that the C subgroup differentiates the purple class and the class shown by the gray arrow together, against all the other classes. In the C subgroup, there is a small separator between the first three markers and the rest of the group: only the first three genes differentiate the two classes against the others. The markers below the separator differentiate between the two classes above the separator, while ignoring all the other classes (since the expression levels in the other classes are ignored by these markers, they are drawn in grey).

A multiclass group

    The D subgroup has a structure similar to the C subgroup, but doesn’t use the same secondary subgroup.
    In some cases, markers appear with a red line on their left border. This means that the complement of the marker was used. (As shown in the E part of the previous figure).