Spanning tree Progression of Density normalized Events (SPADE) is an algorithmic visualization tool for high-dimensional flow and mass cytometry data. The SPADE plugin takes in FCS files and settings, and outputs a network graph file (GML), PDFs of the graphs, and FCS files with the “cluster” column appended.
The SPADE plugin is included with FlowJo v10.1r7 and later. Like all plugins, it requires that version or later to run.
SPADE is implemented as a program in the R statistical computing environment. Therefore, to use SPADE, you must install R and the required R packages onto your computer. To install R on your computer, see the Installing Plugins page on the FlowJo documentation site. Once R is installed, you will no longer need to open R to access SPADE in FlowJo.
The SPADE plugin is included with FlowJo.
If you need to update or re-install SPADE, please see the Installing Plugins page for detailed information on how to obtain and set up FlowJo plugins.
For more detailed instructions on how to use SPADE, refer to the SPADE page on the FlowJo documentation site.