Extracting entire gatingTemplate from GatingSet

[DillonHammill]

Hi @gfinak and @mikejiang,

Is there an easy way to extract the entire gatingTemplate from a GatingSet/GatingHierachy? I am aware of templateGen but I need to extract gating_method and gating_args as well.

Regards, Dillon

[gfinak]

There is no gating method or gating args associated with a gating set. It's not possible to reconstruct the template with full arguments and gating methods directly at this time.

Greg Finak

On Wed, Jul 18, 2018, 18:58 Dillon Hammill notifications@github.com wrote:

Hi @gfinak https://github.com/gfinak and @mikejiang https://github.com/mikejiang,

Is there an easy way to extract the entire gatingTemplate from a GatingSet/GatingHierachy? I am aware of templateGen but I need to extract gating_method and gating_args as well.

Regards, Dillon

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[DillonHammill]

Ok, thank you. I have a workaround for the meantime.

Cheers, Dillon

[DillonHammill]

It would be nice if the add_pop entries were attached to the GatingSet as you add them in a gs@template slot for example. Then the entire template can be extracted from the GatingSet. Maybe this might be possible?

[mikejiang]

add_pop returns a row of the current gating information and you can use rbind to collect and build the template as you go

[DillonHammill]

Hi @mikejiang,

Yes this is how I construct the template normally, I am just wondering if there is way to get this information from the GatingSet directly if you don't have access to the template?

I think I can add the add_pop entries to a new slot in the GatingSet as I construct the gates? something like this...

row <- add_pop(gs, alias, pop, dims etc.)
gs@template <- row

# New entry
row2 <- add_pop(gs, alias, pop, dims etc.)
gs@template <- rbind(gs@template,row2)

# Extract the entire template from gs
template <- gs@template

[mikejiang]

GatingSet was designed as the lower level of data structure that stores the tree of actual gates and intended to be agnostic about how these gates were generated (by template or by parsing xml). I am not sure if it is the best thing to do by adding template information to GatingSet.

[DillonHammill]

I guess the best way is to go through saving and reloading the gatingTemplate csv file?

template <- add_pop(gs, ....)
write.csv(template, "gatingTemplate.csv")

# Load in file and add gate
template <- read.csv("gatingTemplate.csv")
template <- rbind(template, add_pop(gs, ...))

[DillonHammill]

@mikejiang is it possible to extract gates directly from the GatingSet?

[DillonHammill]

getGate() can be used to extract gates from GatingSet