get_clustering_graph_subplan: Get a subplan for graph-based 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 a subplan for graph-based clustering.

Description

Currently supported community-based detection algorithms are:

• igraph::cluster_leiden()

• igraph::cluster_louvain()

• igraph::cluster_walktrap()

See run_graph_based_clustering() for more details.

Usage

get_clustering_graph_subplan(
  sce_target_name,
  dimred,
  cluster_graph_louvain_enabled,
  cluster_graph_louvain_resolutions_,
  cluster_graph_walktrap_enabled,
  cluster_graph_leiden_enabled,
  cluster_graph_leiden_resolutions_,
  cluster_graph_snn_k_,
  cluster_graph_snn_type_,
  is_integration,
  plots_out_dir
)

Arguments

sce_target_name	A character scalar: name of target representing a SCE object that will be used for SNN graph construction.
dimred	A character scalar: which reducedDim() to use for clustering.
cluster_graph_louvain_resolutions_, cluster_graph_leiden_resolutions_	A numeric vector: resolutions to calculate for the selected clustering method.
cluster_graph_leiden_enabled, cluster_graph_louvain_enabled, cluster_graph_walktrap_enabled	A logical scalar: if FALSE, disable the selected clustering and set all corresponding targets to NULL.
cluster_graph_snn_k_, cluster_graph_snn_type_	Passed to graph_snn_fn().
is_integration	A logical scalar: if TRUE, clustering results will be named as ⁠cluster_int_graph_<method>[_r<r>]⁠. If FALSE, they will be named as ⁠cluster_graph_<method>[_r<r>]⁠.
plots_out_dir	A character scalar: path to output directory to save plots (e.g. clustree::clustree()).

Value

drake::drake_plan()

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