tof_metacluster: Metacluster clustered CyTOF data.

In keyes-timothy/tidytof: Analyze High-dimensional Cytometry Data Using Tidy Data Principles

Metacluster clustered CyTOF data.

Description

This function is a wrapper around tidytof's tof_metacluster_* function family. It performs metaclustering on CyTOF data using a user-specified method (of 5 choices) and each method's corresponding input parameters.

Usage

tof_metacluster(
  tof_tibble,
  cluster_col,
  metacluster_cols = where(tof_is_numeric),
  central_tendency_function = stats::median,
  ...,
  augment = TRUE,
  method = c("consensus", "hierarchical", "kmeans", "phenograph", "flowsom")
)

Arguments

tof_tibble	A 'tof_tbl' or 'tibble'.
cluster_col	An unquoted column name indicating which column in 'tof_tibble' stores the cluster ids for the cluster to which each cell belongs. Cluster labels can be produced via any method the user chooses - including manual gating, any of the functions in the 'tof_cluster_*' function family, or any other method.
metacluster_cols	Unquoted column names indicating which columns in 'tof_tibble' to use in computing the metaclusters. Defaults to all numeric columns in 'tof_tibble'. Supports tidyselect helpers.
central_tendency_function	The function that should be used to calculate the measurement of central tendency for each cluster before metaclustering. This function will be used to compute a summary statistic for each input cluster in 'cluster_col' across all columns specified by 'metacluster_cols', and the resulting vector (one for each cluster) will be used as the input for metaclustering. Defaults to median.
...	Additional arguments to pass to the 'tof_metacluster_*' function family member corresponding to the chosen 'method'.
augment	A boolean value indicating if the output should column-bind the metacluster ids of each cell as a new column in 'tof_tibble' (TRUE; the default) or if a single-column tibble including only the metacluster ids should be returned (FALSE).
method	A string indicating which clustering method should be used. Valid values include "consensus", "hierarchical", "kmeans", "phenograph", and "flowsom".

Value

A 'tof_tbl' or 'tibble' If augment = FALSE, it will have a single column encoding the metacluster ids for each cell in 'tof_tibble'. If augment = TRUE, it will have ncol(tof_tibble) + 1 columns: each of the (unaltered) columns in 'tof_tibble' plus an additional column encoding the metacluster ids.

See Also

Other metaclustering functions: tof_metacluster_consensus(), tof_metacluster_flowsom(), tof_metacluster_hierarchical(), tof_metacluster_kmeans(), tof_metacluster_phenograph()

Examples

sim_data <-
    dplyr::tibble(
        cd45 = rnorm(n = 1000),
        cd38 = rnorm(n = 1000),
        cd34 = rnorm(n = 1000),
        cd19 = rnorm(n = 1000),
        cluster_id = sample(letters, size = 1000, replace = TRUE)
    )

tof_metacluster(
    tof_tibble = sim_data,
    cluster_col = cluster_id,
    clustering_algorithm = "consensus",
    method = "flowsom"
)

tof_metacluster(
    tof_tibble = sim_data,
    cluster_col = cluster_id,
    method = "phenograph"
)

keyes-timothy/tidytof documentation built on Aug. 28, 2024, 8:37 a.m.