getTransformations.graphGML fails in my hands AND working with gatingGML outside of flowWorkspace #166
Description
I am trying to follow this documentation:
getTransformations.graphGML package:CytoML R Documentation
Extract transformations from graphGML object.
Description:
Extract transformations from graphGML object.
Usage:
## S3 method for class 'graphGML'
getTransformations(x, ...)
Arguments:
x: graphGML
...: not used
Value:
transformerList object
but I am failing as follows:
> x<-as(graphNEL(),'graphGML')
> getTransformations(x)
Error in UseMethod("getTransformations") :
no applicable method for 'getTransformations' applied to an object of class "c('graphGML', 'graphNEL', 'graph', 'graphBase')"
I encounter this while trying to apply gating from a non-flowJO gatingGML file to a gatingSet, in service of #139.
I wound copying the definition for getTransformations.graphGML into my own function as a temporary workaround, which worked except I am now also coming across a similar issue #30, except in my case
Don't know how to inverse transformation: lintGml2
I am thinking that the whole approach is tailored to working with flowWorkspace and I should perhaps not be trying this approach and I welcome suggestions and/or guidance.