defRootCells {CytoTree} | R Documentation |
definition of root cells
defRootCells(object, root.cells = NULL, verbose = FALSE)
object |
a CYT object |
root.cells |
vector. Cell name of the root 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 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)