tof_cluster_phenograph: Perform PhenoGraph clustering on high-dimensional cytometry...

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

Perform PhenoGraph clustering on high-dimensional cytometry data.

Description

This function performs PhenoGraph clustering on high-dimensional cytometry data using a user-specified selection of input variables/high-dimensional cytometry measurements.

Usage

tof_cluster_phenograph(
  tof_tibble,
  cluster_cols = where(tof_is_numeric),
  num_neighbors = 30,
  distance_function = c("euclidean", "cosine"),
  ...
)

Arguments

tof_tibble	A 'tof_tbl' or 'tibble'.
cluster_cols	Unquoted column names indicating which columns in 'tof_tibble' to use in computing the PhenoGraph clusters. Defaults to all numeric columns in 'tof_tibble'. Supports tidyselect helpers.
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 30.
distance_function	A string indicating which distance function to use for the nearest-neighbor calculation. Options include "euclidean" (the default) and "cosine" distances.
...	Optional additional parameters that can be passed to tof_find_knn.

Details

For additional details about the Phenograph algorithm, see this paper.

Value

A tibble with one column named '.phenograph_cluster'. This column will contain an integer vector of length 'nrow(tof_tibble)' indicating the id of the PhenoGraph cluster to which each cell (i.e. each row) in 'tof_tibble' was assigned.

See Also

Other clustering functions: tof_cluster(), tof_cluster_ddpr(), tof_cluster_flowsom(), tof_cluster_kmeans()

Examples

sim_data <-
    dplyr::tibble(
        cd45 = rnorm(n = 1000),
        cd38 = rnorm(n = 1000),
        cd34 = rnorm(n = 1000),
        cd19 = rnorm(n = 1000)
    )
tof_cluster_phenograph(tof_tibble = sim_data)
tof_cluster_phenograph(tof_tibble = sim_data, cluster_cols = c(cd45, cd19))

keyes-timothy/tidytof documentation built on May 7, 2024, 12:33 p.m.