Get cluster membership for each observation of an umapscan object

Source: R/clustering.R

The clusters taken into account are all the "leaves" of the object clusters tree. If a parent is specified, only the leaves of its subtree are taken.

get_clusters_membership(
  us,
  parent = "",
  max_level,
  noise_inherit_parent = FALSE
)

Arguments

us

umapscan object to describe clusters
parent

name of the parent cluster
max_level

get membership at most this level deep
noise_inherit_parent

if TRUE, 'Noise' points are given their parent cluster membership

See also

compute_clusters(), get_cluster_data(), rename_cluster(), remove_cluster()

Examples

library(dplyr)
iris_num <- iris %>% select_if(is.numeric)
us <- new_umapscan(iris_num, n_neighbors = 25, min_dist = 0.1, seed = 1337)
us <- compute_clusters(us, minPts = 3, eps = 0.5)
get_clusters_membership(us)
#>   [1] "1"       "1"       "1"       "1"       "1"       "1"       "1"      
#>   [8] "1"       "1"       "1"       "1"       "1"       "1"       "1"      
#>  [15] "1"       "1"       "1"       "1"       "1"       "1"       "1"      
#>  [22] "1"       "1"       "1"       "1"       "1"       "1"       "1"      
#>  [29] "1"       "1"       "1"       "1"       "1"       "1"       "1"      
#>  [36] "1"       "1"       "1"       "1"       "1"       "1"       "1"      
#>  [43] "1"       "1"       "1"       "1"       "1"       "1"       "1"      
#>  [50] "1"       "2"       "2"       "2"       "2"       "2"       "2"      
#>  [57] "2"       "2"       "2"       "2"       "2"       "2"       "2"      
#>  [64] "2"       "2"       "2"       "2"       "2"       "2"       "2"      
#>  [71] "2"       "2"       "2"       "2"       "2"       "2"       "2"      
#>  [78] "2"       "2"       "2"       "2"       "2"       "2"       "2"      
#>  [85] "2"       "2"       "2"       "2"       "2"       "2"       "2"      
#>  [92] "2"       "2"       "2"       "2"       "2"       "2"       "2"      
#>  [99] "2"       "2"       "3"       "2"       "3"       "3"       "3"      
#> [106] "3"       "2"       "3"       "3"       "3"       "3"       "3"      
#> [113] "3"       "2"       "2"       "3"       "3"       "3"       "3"      
#> [120] "2"       "3"       "2"       "3"       "2"       "3"       "3"      
#> [127] "2"       "2"       "3"       "3"       "3"       "3"       "3"      
#> [134] "2"       "<Noise>" "3"       "3"       "3"       "2"       "3"      
#> [141] "3"       "3"       "2"       "3"       "3"       "3"       "2"      
#> [148] "3"       "3"       "2"      
us <- compute_clusters(us, minPts = 3, eps = 0.45, parent = "3")
get_clusters_membership(us)
#>   [1] "1"       "1"       "1"       "1"       "1"       "1"       "1"      
#>   [8] "1"       "1"       "1"       "1"       "1"       "1"       "1"      
#>  [15] "1"       "1"       "1"       "1"       "1"       "1"       "1"      
#>  [22] "1"       "1"       "1"       "1"       "1"       "1"       "1"      
#>  [29] "1"       "1"       "1"       "1"       "1"       "1"       "1"      
#>  [36] "1"       "1"       "1"       "1"       "1"       "1"       "1"      
#>  [43] "1"       "1"       "1"       "1"       "1"       "1"       "1"      
#>  [50] "1"       "2"       "2"       "2"       "2"       "2"       "2"      
#>  [57] "2"       "2"       "2"       "2"       "2"       "2"       "2"      
#>  [64] "2"       "2"       "2"       "2"       "2"       "2"       "2"      
#>  [71] "2"       "2"       "2"       "2"       "2"       "2"       "2"      
#>  [78] "2"       "2"       "2"       "2"       "2"       "2"       "2"      
#>  [85] "2"       "2"       "2"       "2"       "2"       "2"       "2"      
#>  [92] "2"       "2"       "2"       "2"       "2"       "2"       "2"      
#>  [99] "2"       "2"       "3_1"     "2"       "3_1"     "3_1"     "3_1"    
#> [106] "3_1"     "2"       "3_1"     "3_1"     "3_1"     "3_1"     "3_1"    
#> [113] "3_1"     "2"       "2"       "3_1"     "3_1"     "3_1"     "3_1"    
#> [120] "2"       "3_1"     "2"       "3_1"     "2"       "3_1"     "3_1"    
#> [127] "2"       "2"       "3_1"     "3_1"     "3_1"     "3_1"     "3_1"    
#> [134] "2"       "<Noise>" "3_1"     "3_1"     "3_1"     "2"       "3_1"    
#> [141] "3_1"     "3_1"     "2"       "3_1"     "3_1"     "3_1"     "2"      
#> [148] "3_1"     "3_1"     "2"      
get_clusters_membership(us, parent = "3")
#>   [1] NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA   
#>  [13] NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA   
#>  [25] NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA   
#>  [37] NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA   
#>  [49] NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA   
#>  [61] NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA   
#>  [73] NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA   
#>  [85] NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA   
#>  [97] NA    NA    NA    NA    "3_1" NA    "3_1" "3_1" "3_1" "3_1" NA    "3_1"
#> [109] "3_1" "3_1" "3_1" "3_1" "3_1" NA    NA    "3_1" "3_1" "3_1" "3_1" NA   
#> [121] "3_1" NA    "3_1" NA    "3_1" "3_1" NA    NA    "3_1" "3_1" "3_1" "3_1"
#> [133] "3_1" NA    NA    "3_1" "3_1" "3_1" NA    "3_1" "3_1" "3_1" NA    "3_1"
#> [145] "3_1" "3_1" NA    "3_1" "3_1" NA