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Filter outliers

cellucid_filter_outlier.Rd

Hide the cells of each category that lie furthest from it in the latent space: those above the threshold quantile (1 hides none).

Usage

cellucid_filter_outlier(viewer, field, threshold)

Arguments

viewer

A viewer cellucid_view() or cellucid_serve() returned.

field

The categorical column the view in focus is coloured by, by name. A named list. Required.

source

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

threshold

The quantile above which cells are hidden; 1 hides none. A number (at least 0, at most 1). 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 filter.outlier (Filters). 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: filters.

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_filter_outlier(viewer, field = list(key = "cell_type",
      source = "obs"), threshold = 0)
  print(request)
  # cellucid_action_result(request) waits for its outcome.
  cellucid_stop(viewer)
}