RGLab/flowCore — pull request #13 by jspidlen (2013-10-16 17:42:57+00:00)
Title: parameters-methods.R don't seem to work for transforms

The unlist(sapply(object@parameters, as, "character"))
that is called from
setMethod("parameters", signature=signature(object="transform"), ...
gives: Error in as.vector(x, "list") : cannot coerce type 'closure' to vector of type 'list'

For the user, this error shows when you read a Gating-ML 1.5 file (i.e., the old one that has been implemented ages ago) that includes a gate that is drawn on a transformed parameter, and than you do something like flowEnv$myGate. This is because the parameter method is called from the show method. It has no effect on how the transform (or the filter that uses the transform) work in terms of filtering sub-populations.

I just fixed it for asinhtGml2 by displaying object@transformationId instead of calling unlist(sapply(object@parameters, as, "character")). This should be sufficient (there are no recursive transformations in Gating-ML 2.0). However, I am not fixing the original Gating-ML 1.5 transforms since I am not completely certain that this would be the best, and I am worried about potential side-effects elsewhere in the code.