Color mapping in FlowJo’s graph window allows users to visualize a third parameter in the two-dimensional display, by illustrating a statistical value for any tertiary parameter in a color scale applied to the dots displayed.

Accessing the Color Map

Checking the box “Color Axis” will display a third parameter by color within the graph window:


You can change the parameter color mapped, using the dropdown list below the color scale. From this list you can choose any parameter associated with a given population:


Statistic Displayed

The parameter displayed using color mapping is actually a statistic of the tertiary parameter, for each bin illustrated. By default the statistic displayed is a Median – This can be altered in the “Color Axis Statistic” area of the graph window:


Advanced Color Mapping

Color mapping dimensionally reduced plots can be particularly powerful for assessing the biology behind unknown clusters. In the following plots tSNE parameters are color mapped by various parameters:






If you have any lingering questions about color mapping in graph windows (or FlowJo in general), we encourage you to write in to: