tof_metacluster_phenograph: Metacluster clustered CyTOF data using PhenoGraph clustering

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

Metacluster clustered CyTOF data using PhenoGraph clustering

Description

This function performs PhenoGraph metaclustering on a 'tof_tbl' containing CyTOF data using a user-specified selection of input variables/CyTOF measurements. The number of metaclusters is automatically detected by the PhenoGraph algorithm. See tof_cluster_phenograph.

Usage

tof_metacluster_phenograph(
  tof_tibble,
  cluster_col,
  metacluster_cols = where(tof_is_numeric),
  central_tendency_function = stats::median,
  num_neighbors = 5L,
  ...
)

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.
num_neighbors	An integer indicating the number of neighbors to use when constructing PhenoGraph's k-nearest-neighbor graph. Smaller values emphasize local graph structure; larger values emphasize global graph structure (and will add time to the computation). Defaults to 5.
...	Optional additional method specifications to pass to tof_cluster_phenograph.

Value

A tibble with a single column ('.phenograph_metacluster') and the same number of rows as the input 'tof_tibble'. Each entry in the column indicates the metacluster label assigned to the same row in 'tof_tibble'.

See Also

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

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_phenograph(tof_tibble = sim_data, cluster_col = cluster_id)

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