optimize_silhouette: Find optimal FindClusters() resolution value to maximize...

In kidcancerlab/rrrSingleCellUtils: A Set of Tools For Single Cell Analysis

Find optimal FindClusters() resolution value to maximize silhouette score

Description

Find optimal FindClusters() resolution value to maximize silhouette score

Usage

optimize_silhouette(
  sobject,
  test_res = seq(0.05, 0.75, by = 0.05),
  summary_plot = TRUE,
  reduction = "pca"
)

Arguments

sobject	A Seurat object containing all of the cells for analysis (required)
test_res	A numeric vector of resolution values to test
summary_plot	A logical value indicating whether to plot the results
reduction	The reduction data used (default is "pca").

Details

This function takes in a Seruat object returns a data frame of silhouette scores for each resolution value

Value

A numeric value

Examples

## Not run: 
optimize_silhouette(sobject = seurat_obj,
                    test_res = seq(0.1, 0.9, by = 0.1))

## End(Not run)

kidcancerlab/rrrSingleCellUtils documentation built on April 17, 2025, 5:10 p.m.