multiSilhouette: Evaluate silhouette indices of clustered single cell data...

View source: R/analysis_functions.R

multiSilhouetteR Documentation

Evaluate silhouette indices of clustered single cell data across several cluster resolutions.

Description

Evaluate silhouette indices of clustered single cell data across several cluster resolutions. Consider running multiCluster(...) first.

Usage

multiSilhouette(
  object,
  groups,
  assay_pattern = NULL,
  assay = NULL,
  verbose = T
)

Arguments

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.

Value

Seurat object

Author(s)

Nicholas Mikolajewicz

See Also

multiCluster

Examples

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()})

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.