defLeafCells: definition of leaf cells

In JhuangLab/CytoTree: A Toolkit for Flow And Mass Cytometry Data

Description

definition of root cells

Usage

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

Arguments

object	a 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

A 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)

JhuangLab/CytoTree documentation built on Nov. 16, 2020, 7:23 a.m.