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).
Options:
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