Change the data mapping

Choose which stored arrays are the embeddings, neighbour graph, genes (modality, expression matrix, gene names, log1p, highly variable), latent space and vector fields; groups not named stay as they are. Applied as one change: refused, nothing changes.

Usage

cellucid_mapping_set(
  viewer,
  embeddings,
  expression,
  gene_names,
  highly_variable,
  knn,
  latent,
  log1p,
  modality,
  vector_fields
)

Arguments

viewer

A viewer cellucid_view() or cellucid_serve() returned.

embeddings

The embeddings views can show, sorted by key then columns, and the default of each dimension. A named list. Left out unless given (the viewer then chooses as its own control does).

enabled

A vector or list of a named list (at least 1 item). Required.

expression

"X", "raw", "layer:<name>", or null for no genes. Text or NULL (at least 1 character). Left out unless given (the viewer then chooses as its own control does).

gene_names

"index", or "column:<var column>". Text (at least 1 character). Left out unless given (the viewer then chooses as its own control does).

highly_variable

The boolean var column marking highly variable genes, or null. Text or NULL (at least 1 character). Left out unless given (the viewer then chooses as its own control does).

knn

The obsp neighbour graph, or null for none. Text or NULL (at least 1 character). Left out unless given (the viewer then chooses as its own control does).

latent

The obsm latent space outlier filters use, or null. Text or NULL (at least 1 character). Left out unless given (the viewer then chooses as its own control does).

log1p

Each expression matrix that holds log1p values, with its base (null: e). A vector or list of a named list. Left out unless given (the viewer then chooses as its own control does).

modality

The modality genes are read from (a dataset of several). Text (at least 1 character). Left out unless given (the viewer then chooses as its own control does).

vector_fields

Vector fields bound to enabled embeddings, sorted by embedding then key. A vector or list of a named list. Left out unless given (the viewer then chooses as its own control does).

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 mapping.set (Data). 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: mapping, views, active-field, filters, colors, camera, 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_mapping_set(viewer)
  print(request)
  # cellucid_action_result(request) waits for its outcome.
  cellucid_stop(viewer)
}