I'm trying to reproduce a FlowJo workflow in flowCore. I received a description of the FlowJo biexponential transform settings from my colleague, which are:

# Minimum is -1622.427; -10^3, no extra negatives
# Maximum is 262144; 10^5
# Width is -100.

The flowCore::biexponentialTransform function has the following call:

biexponentialTransform(transformationId="defaultBiexponentialTransform", 
                       a = 0.5, b = 1, c = 0.5, d = 1, f = 0, w = 0, 
                       tol = .Machine$double.eps^0.25, maxit = as.integer(5000))

And the usage documents don't further elaborate on these parameters.

The logicleTransform function has parameters with values closer to the FlowJo ones:

logicleTransform(transformationId="defaultLogicleTransform", w = 0.5, t = 262144,
                 m = 4.5, a = 0)

Here m=4.5 looks like the 5 decades that I have and t= 262144 matches my maximum. So maybe I should be using logicleTransform instead of biexponentialTransform. But if so, I'm not sure what values to use for w and a. I did try picking some reasonable values (w=0.8 and a=1.0), and my plots come out similarly to the FlowJo plots, but the transformed values end up still being somewhat off, so I'm still not quite there.

You should use flowWorkspace::flowjo_biexp()