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Adding gate_flowclust_2d to gs_pop_add #22

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fbenedett opened this issue Dec 7, 2022 · 0 comments
Open

Adding gate_flowclust_2d to gs_pop_add #22

fbenedett opened this issue Dec 7, 2022 · 0 comments

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@fbenedett
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Dear all,

I have a problem with my gating strategy. Probably it's just because I don't know the proper syntax.
I have done the following with my flowSet "fset":

gs=GatingSet(fset)
rg <- rectangleGate("140Ce"=c(0,10), "DNA1"=c(7, 15), filterId = "Nobead")
gs_pop_add(gs, rg, parent = "root")
recompute(gs)

I can visualize my data after the rectangular gate and see how the flowclust gate behave:

ex <- Subset(fset[[1]], rg)
dna1_and_2gate <- gate_flowclust_2d(ex, "DNA1", "DNA2", filterId = "singlet", K = 1, quantile = 0.99)
ggcyto(ex, aes(x = DNA1, y = DNA2)) + geom_hex(bins = 64) + geom_gate(dna1_and_2gate) + geom_stats()

But how can I add the gate_flowclust_2d to gs_pop_add after the rectangular gate?
Is that even possible? Also, it should be specific for every flow frame.

Thank you for your time.

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