tsne_plot: tsne_plot

In Queen0044/scHiCBayes: Single cell HiC data imputation using Bayesian hierarchy model.

Description

tsne_plot

Usage

tsne_plot(
  data,
  cell_type,
  dims = 2,
  perplexity = 10,
  check_duplicates = FALSE,
  seed = 1234,
  title = NULL,
  kmeans = TRUE,
  ncenters
)

Arguments

data	The observed matrix, with each column being the uppertriangular of a single cell HiC matrix.
cell_type	A vector that indicates cell type.
dims	Integer. Output dimentionality. Default=2.
perplexity	Numeric; Perplexity parameter (should not be bigger than 3 * perplexity < nrow(X) - 1, see details for interpretation).
check_duplicates	Logical; Checks whether duplicates are present. It is best to make sure there are no duplicates present and set this option to FALSE, especially for large datasets (default: TRUE).
seed	Random seed.
title	Title of the plot.
ncenters	Number of clusters in kmeans clustering.

Value

A stne visualization plot.

Examples

tsne_plot(GSE117874_chr1_wo_diag, cell_type=c(rep("GM",14),rep("PBMC",18)), 
dims = 2,perplexity=10, seed=1000, title="Observed GSE117874", 
kmeans = TRUE, ncenters = 2)

Queen0044/scHiCBayes documentation built on Dec. 18, 2021, 8:43 a.m.