Closed malisas closed 3 years ago
How about try skip_faulty_gate = T
?
Hi Mike, thank you for your suggestion! What a timely addition to CytoML.
I'm actually having a bit of trouble installing the latest CytoML version, so for now as a work-around I just ended up generating a list of inconsistent gates via OpenCyto, opening up the demo version of FlowJo 10, and manually deleting all the unwanted gates from the workspace in FlowJo 10. So I'll close this issue for now, but I will try to report back once I troubleshoot/update R and try out skip_faulty_gate = T
. Thanks!
I am trying to load a FlowJo 10 workspace which:
1) Has a lot of unneeded and unwanted gates, 2) Has different gating trees even within the same sample group, and 3) Results in the following error if I set
execute = TRUE
inflowjo_to_gatingset()
, even when loading a single sample (using the subset option):I know that the inconsistent gating trees and the error are all due to gates that I don't care about and are unnecessary. So, I thought that I should try to remove those gates before the gates get computed, in order to avoid the errors:
I tried running
flowjo_to_gatingset
withexecute = FALSE
(great, no more errors!) and was then able to usegroupByTree()
andgs_pop_remove()
in a loop to remove the unwanted nodes and get a consistently gatedGatingSet
, thinking that I could callexecute()
after this step. I noticed that there doesn't seem to be a user-callableexecute()
function, and in fact the documentation forflowjo_to_gatingset()
says:I feel like my situation could benefit from something like an
execute()
function, however.I also tried the combination of the options
execute=TRUE
andincludeGates=FALSE
, thinking I could add the gates later, but then it says:Does anyone have any suggestion for where to find such an
execute()
function, or perhaps some other work-around to get rid of unwanted gates via OpenCyto?Thank you, I hope this is clear!