get_clustering_subplan: Get subplan for clustering.

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Get subplan for clustering.

Description

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:

• get_clustering_graph_subplan()

• get_clustering_kmeans_subplan()

• get_clustering_sc3_subplan()

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.