Hello,

I have been using openCyto to automate gating and we recently updated to one of the last versions.

Doing so, some gates stopped functioning from the gating templates, and few others were broken. Here is my take and how I corrected tmix to make it works, and I would also ask for some guidance given the next directions of your package's implementation if possible.

In gate_quad_tmix function, the tmix filter is first set up and then applied using filter. The problem is that the filter function exists both in stats and in dplyr packages, which seems to break the reference Could it be replaced by an explicit flowCore::filter(...) to avoid issue ?

gate_quad_tmix <- function (...){
...
  tmix_filter <- tmixFilter(parameters = channels, K = K, usePrior = usePrior,
                            prior = prior, trans = trans)
  tmix_results <- try(flowCore::filter(fr, tmix_filter), silent = F) #corrected line adding flowCore reference
...
}

Also, the filter seems not applicable to cytoframes, but only to flowframes. For my use in the gating templates, I took the code of gate_quad_tmix, and implemented the call to flowCore as above, and wrapped it into a registrable function with explicit transformation of the cytoFrame to the flowFrame :

.my_gate_quad_tmix <- function(fr, pp_res, channels = NA, ...){
  #print(channels)
  my_gate_quad_tmix(cytoframe_to_flowFrame(fr), channels = as.character(channels),...)
}

Finally, it was not sufficient for me to just register the name gate_quad_tmix. My wish was to use gate_quad_tmix is for instance with a ' * ' alias to get all populations directly.

alias,     pop,        parent,  dims,       gating_method,  gating_args, ....
"A,B,C,D",  *,          Lymph,  "CH1,CH2",  gate_quad_tmix, K=3,...

The problem is that the function .gating_gtMethod in file gating-methods.R is not understanding it any longer for the gating functions found in one of its line (it wants only +/- +/-, so only one population in alias, not the 4 ones ?)

 if(names(x) %in% c("quadGate.seq", "gate_quad_sequential", "quadGate.tmix", "gate_quad_tmix"))

Hence, I needed to trick the system by providing my own gating function name when registering (I used gate_quad_tmix3, which is pretty poor :-) )

register_plugins(fun = .my_gate_quad_tmix, methodName = "gate_quad_tmix3")

With all of that, I could retrieve the use of a tmix gate usable from a csv gating template, but it was a bit hard :-)

So my questions:

• Would it be possible to have few adjustments in a next release so the openCyto functions can be readily used from a csv gating template?

• Is there anything to know about further developments (e.g. cytoframe vs. flowframe) that would need to be considered when I am updating my stuffs so they would not be deprecated too fast ?

  Lastly, I wanted to thank you for the very nice set of packages in openCyto. Keep up the good work !

Pierre Lebrun