Hello everyone!

I am attempting to use gatingset_to_flowjo() as part of the CytoML package. I pull in compensated fcs files into R as a flowset, change that to a gating set, and then add a few gates using flowWorkspace. When I use gatingset_to_flowjo(), it ends up creating a FlowJo workspace with all the gates and the names of the fcs files of interest, but I am unable to reconnect the FlowJo workspace fcs files to the original fcs files. Therefore, I can only see the gates, but none of the actual events that were originally in the fcs files.

I assume it has something to do with the info message below:

gatingset_to_flowjo(gs, outFile)
INFO: Could not find files for the given pattern(s).
Using docker image public.ecr.aws/x4k5d9i7/cytoverse/gs-to-wsp:latest to write FlowJo workspace...

Is there a way that I can create the .wsp file while also referencing the original fcs files so I can see my data within FlowJo instead of R? I would ultimately like to gate within R but have the ability to manually change the gating positions in FlowJo if necessary.

Thank you for you help in advance!