Embedding: Title Dimension reduction plot (2D) with tsne/umap

In Irenexzwen/SingleCellAnalysisFunc:

Description

Title Dimension reduction plot (2D) with tsne/umap

Usage

Embedding(exprmatx, method = "umap", rdm = 123, n_neighours = 20,
  min_dist = 0.5, perplex = 25, iter = 8000)

Arguments

exprmatx	Dataframe dataframe with each row represents a gene and each column represents a cell
method	str (default tsne). "umap" / "tsne"
rdm	int. (default 123) random seed number for umap (https://umap-learn.readthedocs.io/en/latest/parameters.html).
n_neighours	int. (default=20) param for umap. Higher, more global structure .
min_dist	float. (default=0.1) between 0-1, Higher, more global structure.
perplex	int. default = 25 tsne para.
iter	int. default = 8000 tsne para.

Value

a ggplot object

Examples

p <- Embedding(expr,"umap")

Irenexzwen/SingleCellAnalysisFunc documentation built on Nov. 11, 2020, 10:17 a.m.