Logicle Transform #6
Description
Thanks for the package! The tutorial was very clear and easy to follow and I've found the gating very straightforward for some live-dead cell analyses I'm performing.
Generally, I'm finding this to be a very convenient way to analyze my data. But one problem I've encountered is that the only transformation option for gating (flowjo_biexp) doesn't work well with my dataset.
Here is the plot in ggcyto with logicle transformation (scale_x_logicle() and scale_y_logicle() with default settings) and the gate I drew with the flowjo_biexp transformation applied in the shiny window.
You can see that the gate doesn't fit well around the left side of the data. That is because the flowjo_biexp isn't able to expand this region sufficiently. Here is the figure replotted with the flowjo_biexp transformation. You can see that the right side is much too expanded compared to the left. These are the best settings I could apply (maxValue = 262144, widthBasis = -1, pos = 4.5, neg = 0).
Do you think in a future version of the package it might be possible to choose the logicle transformation during gating rather than flowjo_biexp? I'll probably still use this package, but data analysis will be significantly improved with the option to choose a different transformation.
I'd be happy to share some of my data for development purposes if that would be helpful.