scHiC_tSNE: This function visualize scHi-C data using t-SNE...

In Queen0044/HiCImpute: HiCImpute: An R Package Implementing "Bayesian Hierarchical Model for Identifying Structural Zeros and Enhancing Single-cell Hi-C Data"

This function visualize scHi-C data using t-SNE (t-distributed stochastic neighbor embedding) and applying Kmeans clustering followed by xie et al. 2021.

Description

This function visualize scHi-C data using t-SNE (t-distributed stochastic neighbor embedding) and applying Kmeans clustering followed by xie et al. 2021.

Usage

scHiC_tSNE(
  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

scHiC_tSNE(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/HiCImpute documentation built on Oct. 9, 2022, 9:30 a.m.