Our latest release, FlowJo v10.2, contains new and improved architecture for plugins—giving customers an even greater range of platforms with which to interrogate their data. But first some assembly is required.
Many of these plugins rely on scripts created in the now-infamous R application. While FlowJo (fortunately) does not require users to have an advanced knowledge of R, it does take some setup to get started. After consulting the documentation (see the links below), if you’re unable to generate plugin output, there are some troubleshooting steps you can take:
- Try adjusting the file path to your plugins (in the Diagnostics section of FlowJo's preferences) so that it reads: "/Applications/plugins" on a Mac or “C:\Program Files\FlowJo v10\plugins” on Windows. Additionally, you should make sure that the plugins folder is in fact present in that directory.
- You can also manually enter the R path in FlowJo's preferences. On Windows systems, the default location for R’s bin directory is “C:\Program Files\R\R-3.3.1\bin.” On a Mac, you can open the Mac terminal and enter the command "which r" to find this path. Within the resulting path, copy everything except the "r," and paste that into the R path in FlowJo:
Detailed instructions regarding the process for installing R and the packages required for plugins can be accessed from the following links:
To access R, the following instructions may be helpful:
We also provide specific steps for getting the SPADE package into R here:
Instructions for updating your R to run the flowMeans package can be found on the following documentation page:
Newer versions of Mac OS X are frequently missing an essential dependency called XQuartz (X11) for R to run the FlowMeans plugin. Use the following links to download X11 to your machine.
Mac OS Support page for X11:
X11, XQuartz download:
Our latest suite of plugins can always be accessed from the FlowJo Exchange here:
If you have specific questions or need more help regarding plugins or R, the folks at FlowJo Technical Support would be happy to hear from you: firstname.lastname@example.org.
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