FlowSOM::MetaClustering() throws an error for every method that isn't "metaClustering_consensus"

[keyes-timothy]

In the current version, the FlowSOM::MetaClustering() function throws an error unless the method argument is set to "metaClustering_consensus". Here is a minimal reproducible example:

toy_data <- 
  data.frame(
    marker_1 = runif(n = 100), 
    marker_2 = runif(n = 100), 
    marker_3 = runif(n = 100)
  )

# this runs 
FlowSOM::MetaClustering(
  data = as.matrix(toy_data), 
  method = "metaClustering_consensus"
)
#>   [1] 1 2 3 4 1 3 2 2 3 5 3 2 1 3 3 1 3 2 1 2 2 4 1 4 4 3 2 3 4 1 1 2 3 2 2 2 3
#>  [38] 1 2 2 1 3 1 1 4 4 2 1 3 3 4 2 4 2 3 1 4 1 3 3 4 4 2 1 1 4 3 4 2 2 3 2 1 2
#>  [75] 1 3 3 5 3 2 2 2 2 4 2 2 2 1 2 4 1 2 2 3 1 2 2 2 3 4

# this does not run
FlowSOM::MetaClustering(
  data = as.matrix(toy_data), 
  method = "metaClustering_hclust"
)
#> Error in method(data, k = res, seed = seed): unused argument (seed = seed)

# this does not run
FlowSOM::MetaClustering(
  data = as.matrix(toy_data), 
  method = "metaClustering_som"
)
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> 
#> Mapping data to SOM
#> Error in method(data, k = res, seed = seed): unused argument (seed = seed)

# this does not run
FlowSOM::MetaClustering(
  data = as.matrix(toy_data), 
  method = "metaClustering_kmeans"
)
#> Error in method(data, k = res, seed = seed): unused argument (seed = seed)

To my eye, the reason for this issue is that the third line of the MetaClustering() function calls the subroutines metaClustering_hclust, metaClustering_kmeans, and metaClustering_som with the argument seed, which is not included in any of their function definitions. The following change (or something like it) would fix the problem, though I don't think setting the seed for hierarchical clustering is strictly necessary because it does not involve randomness (I think...!):

metaClustering_hclust <-
  function(data, k = 7, seed) {
    set.seed(seed)
    d <- stats::dist(data, method = "minkowski")
    fit <- stats::hclust(d, method = "ward.D2")
    stats::cutree(fit, k = k)
  }

metaClustering_kmeans <-
  function(data, k = 7, seed) {
    set.seed(seed)
    stats::kmeans(data, centers = k)$cluster
  }

metaClustering_som <-
  function(data, k = 7, seed) {
    set.seed(seed)
    s <- SOM(data ,xdim = k, ydim = 1, rlen = 100)
    s$unit.classif
  }

[artuurC]

Hi,

We addressed this issue in the latest commit. Thank you for bringing this to our attention.
Let us know if you encounter any other issues.

Kind regards
The FlowSOM team

[keyes-timothy]

Awesome! Best of luck with future versions!