getClusters: Determine Optimal Clusters for Gene Expression or Pseudotime...

In ClusterGVis: One-Step to Cluster and Visualize Gene Expression Data

Determine Optimal Clusters for Gene Expression or Pseudotime Data

Description

Determine Optimal Clusters for Gene Expression or Pseudotime Data

Usage

getClusters(obj = NULL, ...)

Arguments

obj	A data object representing the gene expression data or pseudotime data: If the input is a cell_data_set object (e.g., from Monocle3), the function preprocesses the data using pre_pseudotime_matrix. If the input is a numeric matrix or a data.frame, it directly uses this data. Default is NULL.
...	Additional arguments passed to the preprocessing function pre_pseudotime_matrix (e.g., assays, normalize, etc.).

Value

A ggplot object visualizing the Elbow plot, where:

• The x-axis represents the number of clusters tested.

• The y-axis represents the WSS for each cluster number.

The optimal cluster number can be visually identified at the "elbow point," where the reduction in WSS diminishes sharply.

a ggplot.

Author(s)

JunZhang

The getClusters function identifies the optimal number of clusters for a given data object. It supports multiple input types, including gene expression matrices and objects such as cell_data_set. The function implements the Elbow method to evaluate within-cluster sum of squares (WSS) across a range of cluster numbers and visualizes the results.

ClusterGVis documentation built on April 4, 2025, 2:27 a.m.