ConsensusCluster: Keep only HDBSCAN results that pass a certain silhouette...
In CamaraLab/STvEA: Spatially-resolved Transcriptomics via Epitope Anchoring
ConsensusCluster R Documentation
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
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
Usage
ConsensusCluster(
stvea_object,
silhouette_cutoff,
inconsistent_value,
min_cluster_size
)
Arguments
stvea_object
STvEA.data class object after ParameterScan has been run
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.
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| ConsensusCluster | R Documentation |
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
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
Usage
ConsensusCluster(
stvea_object,
silhouette_cutoff,
inconsistent_value,
min_cluster_size
)
Arguments
stvea_object |
STvEA.data class object after ParameterScan has been run |
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 |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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