defLeafCells {CytoTree} | R Documentation |
definition of root cells
defLeafCells(object, leaf.cells = NULL, pseudotime.cutoff = 0, verbose = FALSE)
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. |
A CYT object
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)