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Build the consensus column

cellucid_field_consensus.Rd

The community annotation's consensus for a categorical column as a column of its own: each cell gets the agreed label of its category, or the status of a category without one (disputed, pending); built again under the same name, it is replaced. The outcome of each category is named in the parameters, so it replays by name on any dataset with the same column and categories.

Usage

cellucid_field_consensus(viewer, key, field, mapping, settings, provenance)

Arguments

viewer

A viewer cellucid_view() or cellucid_serve() returned.

key

The consensus column's name. Text (at least 1 character). Required.

field

The annotated column the consensus is of. A named list. Required.

source

Categories belong to columns of the cells. Exactly "obs". Required.

mapping

The outcome of each category of the column (a category left out is pending). A vector or list of a named list (at least 1 item). Required.

settings

The consensus rule it was built with. A named list. Required.

threshold

The net share of votes the leading label needs (-1 to 1). A number (at least -1, at most 1). Required.

provenance

Where the votes came from. A named list. Required.

commit

The commit pulled, when known. Text or NULL (at least 1 character). Required.

pulledAt

When it was last pulled (ISO 8601), null when never. Text or NULL (at least 1 character). Required.

repository

The GitHub repository (owner/name), null when none was connected. Text or NULL (at least 1 character). Required.

Value

A cellucid_action_request, at once and invisibly: the action is sent now, or when the viewer's channel opens. cellucid_action_result(request) returns its outcome (what it did, as names, counts and ids), or NULL when it had nothing to report; request$step is the history step it made.

Details

The viewer's action field.consensus (Fields). It changes the viewer's state: one step of the viewer's history, labelled as R's, undone like any other. The state it can change: field-overlays, active-field, filters, colors.

See also

cellucid_act() sends any action by its type, and cellucid_action_result() collects its answer.

Examples

if (interactive() && requireNamespace("SeuratObject", quietly = TRUE)) {
  data("pbmc_small", package = "SeuratObject")
  viewer <- cellucid_view(SeuratObject::UpdateSeuratObject(pbmc_small))
  request <- cellucid_field_consensus(viewer, field = list(key = "cell_type",
      source = "obs"), key = "x", mapping = list(list(category = "T cells",
      label = "x", status = "consensus", voters = 0)),
      provenance = list(branch = "x", commit = "x", pulledAt = "x",
          repository = "x"), settings = list(minAnnotators = 0,
          threshold = -1))
  print(request)
  # cellucid_action_result(request) waits for its outcome.
  cellucid_stop(viewer)
}