tuneParameters: Optimize Resolution and Gene Number Parameters for Cell Type...

In easybio: Comprehensive Single-Cell Annotation and Transcriptomic Analysis Toolkit

Optimize Resolution and Gene Number Parameters for Cell Type Annotation

Description

This function tunes the resolution parameter in Seurat::FindClusters() and the number of top differential genes (N) to obtain different cell type annotation results. The function generates UMAP plots for each parameter combination, allowing for a comparison of how different settings affect the clustering and annotation.

Usage

tuneParameters(srt, resolution = numeric(), N = integer(), spc)

Arguments

srt	Seurat object, the input data object to be analyzed.
resolution	numeric vector, a vector of resolution values to be tested in Seurat::FindClusters().
N	integer vector, a vector of values indicating the number of top differential genes to be used for matching in matchCellMarker2().
spc	character, the species parameter for the matchCellMarker2() function, specifying the organism.

Value

A list of ggplot2 objects, each representing a UMAP plot generated with a different combination of resolution and N parameters.

easybio documentation built on Sept. 17, 2024, 1:08 a.m.