metaclustering

Assignment of metacluster names to an existing clustering.

Usage

metaclustering(
  fcd,
  cluster_slot,
  cluster_var,
  cluster_var_new = "metacluster",
  metaclusters
)

Arguments

fcd

flow cytometry data set, that has been subjected to clustering with cyCONDOR.

cluster_slot

string specifying which clustering slot to use to find variable specified in cluster_var.

cluster_var

variable name in cluster_slot that contains the original cluster labels.

cluster_var_new

column name that will be used to store the newly assigned cluster labels.

metaclusters

named vector of original cluster labels as names and the corresponding new labels as value, e.g. in case cluster 1 corresponds to T cells and cluster 2 to monocytes use: c("1" = "Tcells", "2" = "Monocytes")

Value

The function adds a new column with the name given in cluster_var_new to the selected cluster_slot. The column contains the new cluster labels (as factors) based on the name to value pairs in metaclusters.

Details

metaclustering

To correctly set up the metaclusters vector, cluster_var needs to be a factor (default after clustering with cyCONDOR). Additionally, the names of the metaclusters vector need to be in the same order as the levels of the factor cluster_var.