defLeafCells {CytoTree}R Documentation

definition of leaf cells

Description

definition of root cells

Usage

defLeafCells(object, leaf.cells = NULL, pseudotime.cutoff = 0, verbose = FALSE)

Arguments

object

an CYT object

leaf.cells

character or numeric. Cell name of the root cells or cluster.id of root.cells

pseudotime.cutoff

numeric. Cutoff of pseudotime. Cells with pseudotime over pseudotime.cutoff will be set to be leaf 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 leaf cells by cluster
cyt <- defLeafCells(cyt, leaf.cells = 1, verbose = TRUE)
cyt <- defLeafCells(cyt, leaf.cells = c(1,3), verbose = TRUE)

# Define root cells by cell names
meta.data <- fetchPlotMeta(cyt)
cells <- meta.data$cell[which(meta.data$stage == "D10")]
cells <- as.character(cells)
cyt <- defLeafCells(cyt, leaf.cells = cells, verbose = TRUE)




[Package CytoTree version 1.4.0 Index]