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Set gene signature options

cellucid_analysis_signature_set.Rd

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

Usage

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

Arguments

viewer

A viewer cellucid_view() or cellucid_serve() returned.

options

A named list. Required.

controlSize

Control genes. A whole number (at least 1). Optional.

geneSets

Gene sets. A vector or list of a named list. Optional.

layout

Sets. One of "side", "each". Optional.

maxRank

Max rank. A whole number (at least 1). Optional.

method

Method. One of "mean", "median", "mean_z", "module", "ucell". Optional.

plotType

Plot. One of "violinplot", "boxplot", "histogram". Optional.

rescale

Rescale. One of "none", "zscore", "minmax". Optional.

seed

Random seed. A whole number (at least 0). 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.signature.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_signature_set(viewer,
      options = list())
  print(request)
  # cellucid_action_result(request) waits for its outcome.
  cellucid_stop(viewer)
}