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ODC-184 support split and duplicated dims in gs_add_gating_method(). #262

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ODC-184 support split and duplicated dims in gs_add_gating_method(). #262

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3 changes: 3 additions & 0 deletions R/add_pop.R
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Original file line number Diff line number Diff line change
Expand Up @@ -77,6 +77,9 @@ gs_add_gating_method <- function(gs, alias = "*"
preprocessing_args <- .argDeparser(preprocessing_args)
}

# format split dims & drop duplicated dims
dims <- paste(unique(dims), collapse = ",")
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Is it OK if dims is more than 2-D?

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openCyto only supports 1D or 2D gating, but yes it will work with more than two dims.

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openCyto/R/csvTemplate-parser.R

Lines 291 to 296 in 323430e

dim_count <- length(strsplit(split = ",", dims)[[1]])
if (!dim_count %in% c(1, 2)) {
if (!(dim_count == 0 && gm %in% c("polyFunctions", "boolGate", "refGate"))) {
stop(popName, " has invalid number of dimensions: ", dim_count)
}
}

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I would love for us to support multiple dims (CytoExploreR uses a hacky way to get around this) but the issue is that the gating functions within openCyto don't perform a dims check so we'd need to update all of them to ensure that appropriate dimensions are supplied for each of the supported gating functions.

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We could possibly check the dims against the list of supported gating methods but that will have to be updated every time we add a new gating method.


thisRow <- data.table(alias = alias
, pop = pop
, parent = parent
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