addEmbedding: addEmbedding

In fungenomics/cytobox: A toolbox for analyzing single cell RNA-seq data

Description

Given a Seurat seurat and a data frame where the rows correspond to cells, in the same order as in the Seurat seurat, add two columns giving coordinates in a dimensionality reduced space.

Usage

addEmbedding(seurat, df, reduction = "tsne", dim1 = 1, dim2 = 2)

Arguments

seurat	Seurat object, where dimensionality reduction has been applied, i.e. (after applying Seurat::RunPCA() or Seurat::RunTSNE() to the object).
df	Data frame with at least one column, "Cell", giving the cell ID
reduction	String specifying the dimensionality reduction to use, retrieves t-SNE by default. This should match the names of the elements of the list seurat@dr, so it will typically be one of "pca" or "tsne". Default: "tsne"

Author(s)

Selin Jessa

Examples

df <- data.frame(Cell = rownames([e-mail]),
                 Cluster = [e-mail]$res.1)

addEmbedding(pbmc, df, reduction = "tsne")

fungenomics/cytobox documentation built on Feb. 13, 2020, 10:51 a.m.