runKmeans {CytoTree} | R Documentation |
Perform k-means clustering on a data matrix.
runKmeans( object, k = 25, iter.max = 10, nstart = 1, algorithm = c("Hartigan-Wong", "Lloyd", "Forgy", "MacQueen"), trace = FALSE, scale = FALSE, verbose = FALSE, ... )
object |
a CYT object |
k |
numeric. The number of clusters. |
iter.max |
numeric. The maximum number of iterations allowed. |
nstart |
numeric. If k is a number, how many random sets should be chosen. |
algorithm |
character. Type of algorithm that will be choosen to calculate kmeans. Four algoritms are provided: Hartigan-Wong, Lloyd, Forgy, MacQueen. |
trace |
logical or integer number. |
scale |
logical. Whether to use scaled data in kmeans. |
verbose |
logical. Whether to print calculation progress. |
... |
Parameters passing to |
a CYT object with kmeans.id in meta.data
cyt.file <- system.file("extdata/cyt.rds", package = "CytoTree") cyt <- readRDS(file = cyt.file) cyt <- runKmeans(cyt, k = 25, verbose = TRUE)