Closed rwbaer closed 2 years ago
cyto_convert()
was originally designed for internal use only - in fact it has been removed from the new version of CytoExploreR. You should not attempt to gate data at the level of a cytoframe
or cytoset
, you should instead use cyto_gatingTemplate_edit()
to add new openCyto
entries to the gatingTemplate
or call gs_add_gating_method()
and update the gatingTemplate
manually afterwards.
Remember, within CytoExploreR
, the gatingTemplate
serves as a means of keeping track of all the gating changes made to your GatingSet
- it is important that any gates applied to your samples are accompanied with an entry in the gatingTemplate
.
@DillonHammill With your help, I think I am now beginning to understand the philosophy behind integrating opencyto gates with cyto_explorer. This should open up more robust ways to analyze data. Your contributions have been really important. Thanks.
Briefly describe what you hope to achieve: I am attempting to automatically draw a quad gate based on all the samples in my gating set and add a node to the nodes I already created in CytoExploreR manually.
I had intended to use gate_quad_sequential() from the openCyto package and then gs_pop_add from the flowworkspace package.
Since gate_quad_sequential() requires a flow frame I tried to use cyto_convert from CytoExploreR to collapse the gating set into a single flow frame, but I seem to end up with an empty flow frame. Clearly, I'm doing something wrong. I was expecting the result to based on root node.
Any suggestions on how to approach such a task? What am I misunderstanding about cyto_convert?
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