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ODC-188 drop legacy GatingSetList from openCyto test suite. #266

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ODC-188 drop legacy GatingSetList from openCyto test suite. #266

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82ea7ce
ODC-188 drop legacy GatingSetList from openCyto test suite.
djhammill Nov 6, 2024
fc4ca4e
ODC-188 get channel markers for each channel separately in gt_gating().
djhammill Nov 6, 2024
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7 changes: 6 additions & 1 deletion R/gating-methods.R
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Original file line number Diff line number Diff line change
Expand Up @@ -583,7 +583,12 @@ gt_gating.dummyMethod <- function(x, y, ...) {
# standardize the names for the gate parameters and dims
gate_params <- unlist(lapply(glist, function(g) {
cur_param <- parameters(g)
getChannelMarker(fr, cur_param)["name"]
sapply(
cur_param,
function(param) {
getChannelMarker(fr, param)["name"]
}
)
}))
negated_2d_gate <- FALSE
if(length(glist)==1){
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4 changes: 2 additions & 2 deletions tests/testthat/test-add-remove-pop.R
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Expand Up @@ -28,9 +28,9 @@ test_that("gs_remove_gating_method testing", {
gs_remove_gating_method(gs)
gs_remove_gating_method(gs)

# Just to prevent GatingSetList constructor from protesting overlapping samples
# Just to prevent merge_list_to_gs constructor from protesting overlapping samples
sampleNames(gs2) <- "CytoTrol_Cytotrol_2.fcs"
gslist <- GatingSetList(list(gs1, gs2))
gslist <- merge_list_to_gs(list(gs1, gs2))

expect_equal(gs_get_pop_paths(gslist[[1]]), snapshot_pre)
gs_add_gating_method(gslist, alias = "*", pop = "+/-", parent = "/not debris", dims = "CD4", gating_method = "mindensity")
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