ConsensusCluster.internal: Keep only HDBSCAN results that pass a certain silhouette...

In CamaraLab/STvEA: Spatially-resolved Transcriptomics via Epitope Anchoring

Keep only HDBSCAN results that pass a certain silhouette score cutoff and create a dissimilarity matrix between cells from the clusterings Perform agglomerative hierarchical clustering on the consensus dissimilarity matrix Takes matrices and data frames instead of STvEA.data class

Description

Keep only HDBSCAN results that pass a certain silhouette score cutoff and create a dissimilarity matrix between cells from the clusterings Perform agglomerative hierarchical clustering on the consensus dissimilarity matrix Takes matrices and data frames instead of STvEA.data class

Usage

ConsensusCluster.internal(
  hdbscan_results,
  cite_latent,
  silhouette_cutoff,
  inconsistent_value,
  min_cluster_size
)

Arguments

hdbscan_results	output of ParameterScan.internal
cite_latent	CITE-seq latent space (cells x dimensions)
silhouette_cutoff	minimum silhouette score to keep clustering
inconsistent_value	input parameter to python fcluster determining where clusters are cut in the hierarchical tree
min_cluster_size	cells in clusters smaller than this value are assigned a cluster ID of -1, indicating no cluster assignment

CamaraLab/STvEA documentation built on April 2, 2024, 6:07 a.m.