defRootCells {CytoTree}R Documentation

definition of root cells

Description

definition of root cells

Usage

defRootCells(object, root.cells = NULL, verbose = FALSE)

Arguments

object

an CYT object

root.cells

vector. Cell name of the root cells

verbose

logical. Whether to print calculation progress.

Value

An CYT object

Examples


cyt.file <- system.file("extdata/cyt.rds", package = "CytoTree")
cyt <- readRDS(file = cyt.file)

# Define root cells by cluster
cyt <- defRootCells(cyt, root.cells = 6, verbose = TRUE)
cyt <- defRootCells(cyt, root.cells = c(6,8), verbose = TRUE)

# Define root cells by cell names
meta.data <- fetchPlotMeta(cyt)
cells <- meta.data$cell[which(meta.data$stage == "D0")]
cells <- as.character(cells)
cyt <- defRootCells(cyt, root.cells = cells, verbose = TRUE)
[Package CytoTree version 1.2.0 Index]