The Advanced color settings offer settings for changing the color of the plot objects. To choose a color used on all objects, choose "Fixed Color" in the "Options" field. This color can be selected in three different ways: by "Samples", by "HSB" or by "RGB", available under three different tabs in the "Fixed color" field. Below this field there is a "Preview" field.

To set the objects to be "Continuous by Index" or "Continuous by Value" select this under "Options" and then select which color scale you wish to use. By default, the scale ranges from minimum value to maximum value. Using "Reverse" will swap the color scale to be the opposite. By selecting "Range limits" the user can choose between which values the continuous color scale should span. Values below or above this range will receive the color representing the minimum or the maximum value respectively. If "Continuous by Value" is selected, the tab "Color Source" will be activated. The user can here select a different matrix or vector to use for coloring.

The color "By Category" option contains a combo-box for choosing which category to color, and a combo-box for choosing which color scheme to use. Choosing "Custom" will enable the user to choose exactly which color each class should have. By clicking on the color bars, a color selection panel will appear where the user can choose color by either "Samples", "HSB" or "RGB". It is also possible to choose a predefined color scale such as "Hot", "Summer" or "Cool". These color scales can be reversible by checking the "Reverse colors" option. The "Prediction Category" option is available if the plot originates from predicted data.

"Continuous by Density" sets the color according to how densely the plot objects are populated. Objects with very few neighbors will have the color set according to "Min", while the most densely populated areas of the plot will have objects set to "Max". The user can also reverse the color scale.