Set marker genes options

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

Usage

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

Arguments

viewer

A viewer cellucid_view() or cellucid_serve() returned.

options

A named list. Required.

compareAgainst

Compare against. One of "rest", "group". Optional.

correction

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

direction

Direction. One of "up", "down", "both". Optional.

excludeGenes

Exclude genes. A vector or list of text (each once). Optional.

excludePattern

Exclude pattern. Text. Optional.

foldChange

Fold change from. One of "auto", "log1p", "stored". Optional.

groupBy

Group by. Text. Optional.

matrix

Expression matrix. Text. Optional.

maxAdjP

Max adjusted p. A number (at least 0, at most 1). Optional.

maxPctRef

Max % in reference. A number (at least 0, at most 100). Optional.

method

Method. One of "wilcox", "ttest", "ttest_overestim_var". Optional.

minCells

Min cells per group. A whole number (at least 2). Optional.

minLog2FC

Min |log2FC|. A number (at least 0). Optional.

minPctIn

Min % expressing in group. A number (at least 0, at most 100). Optional.

onlyGenes

Only genes in. Text. Optional.

onlyGenesList

Gene list. Text. Optional.

pConvention

Wilcoxon p-values. One of "exact", "normal", "normal_tie". Optional.

rankBy

Rank by. One of "score", "padj", "log2fc", "auroc", "pct_diff". Optional.

referenceGroup

Reference group. Text. Optional.

restIncludes

Rest includes. One of "all", "selected". Optional.

smallGroups

Small groups. One of "skip", "pool", "test". Optional.

testGroups

Groups to test: 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.

topN

Top genes per group. A whole number (at least 1). 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.markers.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_markers_set(viewer, options = list())
  print(request)
  # cellucid_action_result(request) waits for its outcome.
  cellucid_stop(viewer)
}