tof_annotate_clusters: Manually annotate tidytof-computed clusters using...

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

Manually annotate tidytof-computed clusters using user-specified labels

Description

This function adds an additional column to a 'tibble' or 'tof_tbl' to allow users to incorporate manual cell type labels for clusters identified using unsupervised algorithms.

Usage

tof_annotate_clusters(tof_tibble, cluster_col, annotations)

Arguments

tof_tibble	'tof_tbl' or 'tibble'.
cluster_col	An unquoted column name indicating which column in 'tof_tibble' contains the ids of the unsupervised 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.
annotations	A data structure indicating how to annotate each cluster id in 'cluster_col'. 'annotations' can be provided as a data.frame with two columns (the first should have the same name as 'cluster_col' and contain each unique cluster id; the second can have any name and should contain a character vector indicating which manual annotation should be matched with each cluster id in the first column). 'annotations' can also be provided as a named character vector; in this case, each entry in 'annotations' should be a unique cluster id, and the names for each entry should be the corresponding manual cluster annotation. See below for examples.

Value

A 'tof_tbl' with the same number of rows as 'tof_tibble' and one additional column containing the manual cluster annotations for each cell (as a character vector). If 'annotations' was provided as a data.frame, the new column will have the same name as the column containing the cluster annotations in 'annotations'. If 'annotations' was provided as a named character vector, the new column will be named '{cluster_col}_annotation'.

Examples

sim_data <-
    dplyr::tibble(
        cd45 = rnorm(n = 1000),
        cd38 = c(rnorm(n = 500), rnorm(n = 500, mean = 2)),
        cd34 = c(rnorm(n = 500), rnorm(n = 500, mean = 4)),
        cd19 = rnorm(n = 1000),
        cluster_id = c(rep("a", 500), rep("b", 500))
    )

# using named character vector
sim_data |>
    tof_annotate_clusters(
        cluster_col = cluster_id,
        annotations = c("macrophage" = "a", "dendritic cell" = "b")
    )

# using two-column data.frame
annotation_data_frame <-
    data.frame(
        cluster_id = c("a", "b"),
        cluster_annotation = c("macrophage", "dendritic cell")
    )

sim_data |>
    tof_annotate_clusters(
        cluster_col = cluster_id,
        annotations = annotation_data_frame
    )

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