make_trees: Convert An Expression Matrix into Tree Format

In duohongrui/simutils: Common functions used in data simulation and evaluation

Convert An Expression Matrix into Tree Format

Description

This function is used to convert the gene expression matrix into the tree format.

Usage

make_trees(
  ref_data,
  group = NULL,
  is_Newick = TRUE,
  is_parenthetic = FALSE,
  return_group = FALSE
)

Arguments

ref_data	A Matrix. The gene expression matrix where every row represents a cell and every column represents a gene.
group	A Vector. The group information of the cells in ref_data
is_Newick	If TRUE, return the Newick format.
is_parenthetic	If TRUE, return the parenthetic format.
return_group	Whether to return the group information of cells.

Value

A file of parenthetic format or Newick format

Examples

ref_data <- matrix(rpois(n = 2500, lambda = 2), nrow = 50)
rownames(ref_data) <- paste0("cell_", 1:ncol(ref_data))
colnames(ref_data) <- paste0("gene_", 1:nrow(ref_data))
group <- c(rep("A", 15), rep("B", 5), rep("C", 20), rep("D", 10))
tree_format <- make_trees(ref_data, group = group)

duohongrui/simutils documentation built on March 12, 2024, 8:40 p.m.