Graphs button in the Preferences tool to open the Graphs preferences. Descriptions are broken into sections below.



Graph Type:

Graph Type : Set the default graph type for all newly created graphs.

Contour Levels : Set the percentage of cells that each contour line represents, or switch to logarithmic scaling of the

contour lines.

Smooth : If checked the spaces between data points will be filled with a gradual transition, generally using color.

Foreground Color : Set the color of the lines and dots used in drawing graphs.

Show Outliers : If checked, events outside of a smoothed representation of the data will be plotted as dots.

Background Color : Set the color of the filled space underneath graphs.

Histogram Scaling : Set the Y-axis scaling for histograms to either be scaled to the number of events or relative to the mode of the number of events.

Stroke : Set the line weight for the selected figure(s).


Show Forward Scatter on X Axis : Will display forward scatter on X axis on all new plots.

Show Event Number Parameter : Add a parameter showing the events’ position within the data file

Show Uncompensated Parameters : If the file in compensated, define whether parameter menus include both

compensated and uncompensated versions of each parameter.

Show Background Grid : If checked the graph will display lines extending the major ticks,

Number of dots drawn (0=all) : Select the MAXIMUM number of dots to display in a dot plot. Entering a 0 displays all

events. Entering a number between 1 and 100 displays that percentage of events.

Show Warning if too many events on Axis :  If the number of events on either axis exceeds the specified threshold,

FlowJo will display warning text.

Draw Large Dots : If checked, FlowJo will draw slightly bigger dots on dot plots.

3D View:

Dot Color:  Set default dot color.

Foreground:  Set default foreground color in the 3D platform.

Labels: Set default label color for axis labeling

Background: Set default background color in the 3D cube

Maximum Points in Bubble Plot: Set the default points in a bubble plot.

Plot Resolution: Set default plot resolution