getReductionCentroids: Calculate seurat cluster centroids based on a Dimensional...

In APackOfTheClones: Visualization of Clonal Expansion for Single Cell Immune Profiles

Calculate seurat cluster centroids based on a Dimensional reduction

Description

Utility function to calculate the physical xy coordinates of each seurat cluster based on a dimensional reduction already present in the object. The results are returned in a list with the length of the number of distinct seurat clusters based on the seurat_obj meta.data.

Usage

getReductionCentroids(seurat_obj, reduction)

Arguments

seurat_obj	input seurat object with the dimensional reduction of choice already present, and seurat clusters computed.
reduction	character. The reduction that the centroid calculation should be based on.

Value

A list of the length of the number of distinct clusters in the seurat object metadata, where each element of the list is a numeric vector of length 2, with the numbers corresponding to the x and y coordinate respectively of the seurat cluster with the corresponding index.

Examples

data("combined_pbmc")
getReductionCentroids(combined_pbmc, reduction = "umap")

APackOfTheClones documentation built on Oct. 11, 2024, 1:08 a.m.