Merge pull request #441 from Qile0317/e2l

re-export expression2List() with deprecation message

NAMESPACE

@@ -24,6 +24,7 @@ export(combineExpression)
 export(combineTCR)
 export(createHTOContigList)
 export(exportClones)
+export(expression2List)
 export(getCirclize)
 export(getContigDoublets)
 export(highlightClones)

R/deprecated.R

@@ -0,0 +1,43 @@
+#' ***DEPRECATED*** Take the meta data in seurat/SCE and place it into a list
+#'
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#'
+#' Allows users to perform more fundamental measures of clonotype analysis
+#' using the meta data from the seurat or SCE object. For Seurat objects the
+#' active identity is automatically added as "cluster". Remaining grouping
+#' parameters or SCE or Seurat objects must appear in the meta data.
+#'
+#' This function is deprecated as of version 2 due to the confusion it caused
+#' to many users. Users are encouraged to remain with the abstraction barrier
+#' of combined single cell objects and the outputs of [combineTCR()] and
+#' [combineBCR()] for all functions.
+#'
+#' We discourage the use of this function, but if you have to use it, set the
+#' `force` argument to `TRUE`.
+#'
+#' @param sc output of [combineExpression()].
+#' @param ... previously the `group` or `split.by` argument, indicating the
+#' column header to group the new list by. This should strictly be one argument
+#' and is an ellipsis for backwards compatibility. Everything after the first
+#' argument is ignored.
+#' @param force logical. If not `TRUE` (default), a deprecation error will
+#' be thrown. Otherwise the function will run but not guaranteed to be stable.
+#'
+#' @export
+#' @return list derived from the meta data of single-cell object with
+#' elements divided by the group parameter
+#' @keywords internal
+#'
+expression2List <- function(sc, ..., force = FALSE) {
+
+    if (!force) {
+        lifecycle::deprecate_stop(
+            "2.0.0", "expression2List()",
+            details = "If you MUST use it, see `?expression2List`"
+        )
+    }
+
+    lifecycle::deprecate_soft("2.0.0", "expression2List()")
+    .expression2List(sc, list(...)[[1]])
+}