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Set composition options

cellucid_analysis_composition_set.Rd

Change options of the composition analysis (only those given); nothing runs.

Usage

cellucid_analysis_composition_set(viewer, options, in_ = "panel", show = FALSE)

Arguments

viewer

A viewer cellucid_view() or cellucid_serve() returned.

options

A named list. Required.

cellTypes

Cell types. Text. Optional.

cells

Cells. Text. Optional.

condition

Condition. Text. Optional.

correction

Multiple testing. One of "bh", "bonferroni". Optional.

method

Test. One of "logit", "rank", "clr". Optional.

onlyTypes

Only these cell types: all, or the categories (or pages) by name. Either a named list; or a named list. Optional.

ids

A vector or list of text (at least 1 character) (each once). Required.

order

Cell type order. One of "field", "abundance", "change". Optional.

samples

Samples. Text. Optional.

values

Show. One of "proportion", "count". Optional.

in_

Either exactly "panel" (The Analysis panel); or a whole number (at least 1) (A floating analysis window, by its number (1 is the first open)). Default "panel", the viewer's own. Sent as the parameter in.

show

Also open it in the Analysis panel (with in "panel"), as another analysis's "send to" does. TRUE or FALSE. Default FALSE, the viewer's own.

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 analysis.composition.set (Analysis). 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: analysis.

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_analysis_composition_set(viewer,
      options = list())
  print(request)
  # cellucid_action_result(request) waits for its outcome.
  cellucid_stop(viewer)
}