tof_cluster_grouped: Cluster (grouped) high-dimensional cytometry data.

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

Cluster (grouped) high-dimensional cytometry data.

Description

This function is a wrapper around tidytof's tof_cluster_* function family and provides a low-level API for clustering grouped data frames. It is a subroutine of tof_cluster and shouldn't be called directly by users.

Usage

tof_cluster_grouped(tof_tibble, group_cols, ..., augment = TRUE, method)

Arguments

tof_tibble	A 'tof_tbl' or 'tibble'.
group_cols	An unquoted column name indicating which columns should be used to group cells before clustering. Clustering is then performed on each group independently.
...	Additional arguments to pass to the 'tof_cluster_*' function family member corresponding to the chosen method.
augment	A boolean value indicating if the output should column-bind the cluster ids of each cell as a new column in 'tof_tibble' (TRUE, the default) or if a single-column tibble including only the cluster ids should be returned (FALSE).
method	A string indicating which clustering methods should be used. Valid values include "flowsom", "phenograph", "kmeans", "ddpr", and "xshift".

Value

A 'tof_tbl' or 'tibble' If augment = FALSE, it will have a single column encoding the cluster 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 cluster ids.

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