View source: R/analysis_functions.R
multiSilhouette | R Documentation |
Evaluate silhouette indices of clustered single cell data across several cluster resolutions. Consider running multiCluster(...) first.
multiSilhouette(
object,
groups,
assay_pattern = NULL,
assay = NULL,
verbose = T
)
object |
Seurat object with multi-resolution clusters provided in meta data. |
groups |
Vector specifying names of all cluster configurations found in meta data. |
assay_pattern |
Cluster naming prefix. |
assay |
Seurat assay used for clustering. If not specified, default assay is used. |
verbose |
Print progress. Default is TRUE. |
Seurat object
Nicholas Mikolajewicz
multiCluster
msil_list <- multiSilhouette(object = so.query, groups = cluster.name, assay_pattern = assay.pattern, verbose = T)
sil.plot <- msil_list$silhouette_plots
plt.silw.dep <- msil_list$resolution_plot
df.silw <- msil_list$silhouette_raw
df.silw.sum <- msil_list$silhouette_summary
rm(msil_list); invisible({gc()})
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