FindConnectedComponents

Inspects an SNN (or any named) graph from a Seurat object and labels each cell by its connected component. The result is written to a new column in seurat_obj@meta.data. This is a useful diagnostic before running PerturbationTransitions, because cells that belong to different connected components cannot exchange transition probability mass through the graph.

Usage

FindConnectedComponents(
  seurat_obj,
  graph = NULL,
  meta_data_name = "connected_component",
  verbose = TRUE
)

Arguments

seurat_obj

A Seurat object containing at least one graph in seurat_obj@graphs.

graph

Character. Name of the graph in Graphs(seurat_obj) to analyse. If NULL (default), the function auto-detects a graph whose name ends in "_snn". When multiple SNN graphs exist the first one is used and a message is emitted. If no SNN graph is present the first available graph is used instead (with a warning).

meta_data_name

Character. Name of the new column written to seurat_obj@meta.data. Default "connected_component".

verbose

Logical. Print a summary of the component structure. Default TRUE.

Value

The Seurat object with a new integer-factor column in seurat_obj@meta.data. Levels are ordered by component size (largest component = level 1) so the dominant component always has the lowest label.

Details

The graph is treated as undirected for component finding — any non-zero edge weight is interpreted as a connection. The underlying computation uses igraph::components(), which implements a fast depth-first-search.