ggcyto provides the interesting axis_x_inverse_trans and axis_y_inverse_trans functions to allow for a visualization more familiar to FlowJo users.
I am not completely certain, but I assume that this function takes its information from the `axis` attribute stored in the gatingSet (based on the data in this tutorial: https://www.bioconductor.org/help/course-materials/2015/BioC2015/ggcyto.html). Is there a way to automatically create this attribute from transformations applied in R and not imported from a FlowJo workspace, or to apply a transformation directly to a GatingSet? In particular, my workflow involves estimating the logicle transforms for fluorescence channels, applying this transformation via transform() and then instantiating a GatingSet for this transformed data.
I actually hacked together a solution that adjusts the labels of the transformed axis back into the untransformed space and provides logticks, based on a channel and an transformList generated by estimateLogicle, but neither the approach, nor my implementation are elegant by any stretch of the imagination. If there is a more suitable way that I might have missed, I would be glad to learn about it.
