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]