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Get subplan for clustering.

Source: R/plans_common_clustering.R
get_clustering_subplan.Rd

Besides clustering itself, this plan also includes dimred plots of computed clusters.

Usage

get_clustering_subplan(
  cfg,
  sce_clustering_target_name,
  sce_dimred_plots_target_name,
  dimred,
  report_dimred_names,
  dimred_plots_out_dir,
  other_plots_out_dir,
  is_integration,
  spatial,
  seed = 1
)

Arguments

cfg

A list of parameters for 02_norm_clustering or 02_int_clustering stage.

sce_clustering_target_name, sce_dimred_plots_target_name

A character scalar: name of target representing a SCE object that will be used for SC3 clustering and dimred plots, respectively.

dimred

A character scalar: which reducedDim() to use for clustering. This is only applied to graph-based and k-means clustering.

report_dimred_names

A character vector: dimreds to use for plotting clustering results.

dimred_plots_out_dir, other_plots_out_dir

A character scalar: path to output directory to save plots.

is_integration

A logical scalar: if TRUE, clustering results will be named with cluster_int_* prefix.

spatial

A logical scalar: if TRUE, enabling pseudotissue spatial visualization for spatial transcriptomics datasets.

seed

An integer scalar: random seed for SC3.

Value

A combined drake::drake_plan() from: