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Set dot plot options

cellucid_analysis_dotplot_set.Rd

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

Usage

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

Arguments

viewer

A viewer cellucid_view() or cellucid_serve() returned.

options

A named list. Required.

colorMap

Color map. One of "Reds", "Viridis", "Blues". Optional.

cutoff

Expressed above. A number. Optional.

geneSets

Genes. A vector or list of a named list. Optional.

groupBy

Group by. Text. Optional.

groupOrder

Group order. One of "field", "size", "dendrogram". Optional.

groups

Groups to show: 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.

matrix

Expression matrix. Text. Optional.

maxDotSize

Largest dot. One of "auto", "12", "18", "24", "32". Optional.

meanOnlyExpressing

Mean of expressing cells only. TRUE or FALSE. Optional.

plot

Plot. One of "dot", "matrix", "violin". Optional.

scale

Color. One of "none", "var", "z". Optional.

swapAxes

Genes down, groups across. TRUE or FALSE. 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.dotplot.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_dotplot_set(viewer, options = list())
  print(request)
  # cellucid_action_result(request) waits for its outcome.
  cellucid_stop(viewer)
}