tsneFromDistane: tsneFromDistane.Seurat

In WilsonImmunologyLab/LinQView: Integrate information from both transcriptome and cell surface protein signals to better identify cell heterogeneity

Description

Run t-SNE to project single cells into 2D map using cell-cell pairwise distances

Usage

## S3 method for class 'Seurat'
tsneFromDistane(
  object,
  assay = "All",
  perplexity = 30,
  dim = 2,
  seed = 42,
  theta = 0.5
)

## Default S3 method:
tsneFromDistane(object, perplexity = 30, dim = 2, seed = 42, theta = 0.5)

tsneFromDistane(object, ...)

Arguments

object	(For Seurat) Seurat object
assay	(For Seurat) run t-SNE for which assay, choose from RNA, ADT, Joint or All
perplexity	numeric; Perplexity parameter (should not be bigger than 3 * perplexity < nrow(X) - 1, see details for interpretation)
dim	integer; Output dimensionality (default: 2)
seed	integer; seed for reproducible results.
theta	numeric; Speed/accuracy trade-off (increase for less accuracy), set to 0.0 for exact TSNE (default: 0.5)

WilsonImmunologyLab/LinQView documentation built on Jan. 3, 2022, 10 p.m.