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 and Overlay Settings
Overlay Mode: Allows the user to select what type of y axis scaling will be used as the default histogram scaling when histograms are overlayed.
Line: Controls the default histogram line thickness.
Fill: Controls the default tint inside the histogram.
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.