PartitionSimilarityGraph: Create a graph of cosine similarities between clusters pruned...

In yanwu2014/swne: Similarity Weighted Nonnegative Embedding: A method for visualizing high dimensional datasets

Create a graph of cosine similarities between clusters pruned using PAGA

Description

Create a graph of cosine similarities between clusters pruned using PAGA

Usage

PartitionSimilarityGraph(
  partitions,
  embedding,
  qval.cutoff = 0.001,
  min.cluster.sim = 0.05,
  seed = 42
)

Arguments

partitions	List representing a PAGA graph (output of BuildPAGA)
qval.cutoff	Q-value cutoff for cluster to cluster interactions
min.cluster.sim	Minimum similarity needed to draw an edge between two clusters
seed	Random seed for force-directed layout reproducibility
embeddings	Dimensional reduction used to compute cosine similarities (cells x dimensions)

Value

igraph object where each vertex is a cluster and edges represent PAGA-pruned similarities between clusters

yanwu2014/swne documentation built on Aug. 5, 2023, 4:42 a.m.