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Build the intensity transform the whole run uses

Source: R/transform-methods.R
make_transform.Rd

WHAT IT RETURNS: an object with fn(x, marker), so every call site applies the transform the same way and none of them needs to know which method is in force. Adding a method here reaches the gating, scoring, embedding and figure code without touching any of them.

Usage

make_transform(
  method = c("arcsinh", "logicle", "none"),
  cofactor = NULL,
  logicle = NULL,
  per_marker = NULL
)

Arguments

method

"arcsinh", "logicle" or "none"

cofactor

arcsinh cofactor (required for method = "arcsinh")

logicle

named list of per-marker parameters from derive_logicle_pooled() (required for method = "logicle")

per_marker

named numeric vector of arcsinh cofactors by marker, or NULL. A marker named here is transformed with its own cofactor; any other, and scatter, with cofactor. See derive_cofactor().

Value

list(method, fn, params, label)