A system comprising: an output device configured to display an interface; a controller configured to generate a tree plot representing binned polychromatic flow cytometry data, wherein the flow cytometry data includes at least classified data, wherein the output device is further configured to display the tree plot within the interface; and an input device configured to allow selection of a portion of the displayed tree plot, wherein: the controller is further configured to generate at least one of a histogram, a contour plot, a density plot, a radar plot, or a scatter plot; the output device is further configured to display the at least one of the histogram, the contour plot, the density plot, the radar plot, or the scatter plot within the interface; the input device is further configured to allow selection of one or more portions of the at least one of the histogram, the contour plot, the density plot, the radar plot, or the scatter plot displayed by the output device; the controller is further configured to generate an updated tree plot; the updated tree plot comprises a phenotypic tree plot representing a sub-set of binned polychromatic flow cytometry data corresponding to the one or more selected portions of the at least one of the histogram, the contour plot, the density plot, the radar plot, or the scatter plot; and the output device is further configured to display the updated tree plot substantially immediately within the interface. an output device configured to display an interface; a controller configured to generate a tree plot representing binned polychromatic flow cytometry data, wherein the flow cytometry data includes at least classified data, wherein the output device is further configured to display the tree plot within the interface; and an input device configured to allow selection of a portion of the displayed tree plot, wherein: the controller is further configured to generate at least one of a histogram, a contour plot, a density plot, a radar plot, or a scatter plot; the output device is further configured to display the at least one of the histogram, the contour plot, the density plot, the radar plot, or the scatter plot within the interface; the input device is further configured to allow selection of one or more portions of the at least one of the histogram, the contour plot, the density plot, the radar plot, or the scatter plot displayed by the output device; the controller is further configured to generate an updated tree plot; the updated tree plot comprises a phenotypic tree plot representing a sub-set of binned polychromatic flow cytometry data corresponding to the one or more selected portions of the at least one of the histogram, the contour plot, the density plot, the radar plot, or the scatter plot; and the output device is further configured to display the updated tree plot substantially immediately within the interface. the controller is further configured to generate at least one of a histogram, a contour plot, a density plot, a radar plot, or a scatter plot; the output device is further configured to display the at least one of the histogram, the contour plot, the density plot, the radar plot, or the scatter plot within the interface; the input device is further configured to allow selection of one or more portions of the at least one of the histogram, the contour plot, the density plot, the radar plot, or the scatter plot displayed by the output device; the controller is further configured to generate an updated tree plot; the updated tree plot comprises a phenotypic tree plot representing a sub-set of binned polychromatic flow cytometry data corresponding to the one or more selected portions of the at least one of the histogram, the contour plot, the density plot, the radar plot, or the scatter plot; and the output device is further configured to display the updated tree plot substantially immediately within the interface.