tof_upsample_neighbor: Upsample cells into the cluster of their nearest neighbor a...

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

Upsample cells into the cluster of their nearest neighbor a reference dataset

Description

This function performs upsampling on CyTOF data by sorting single cells (passed into the function as 'tof_tibble') into their most phenotypically similar cell subpopulation in a reference dataset (passed into the function as 'reference_tibble'). It does so by finding each cell in ‘tof_tibble'’s nearest neighbor in 'reference_tibble' and assigning it to the cluster to which its nearest neighbor belongs. The nearest neighbor calculation can be performed with either euclidean or cosine distance.

Usage

tof_upsample_neighbor(
  tof_tibble,
  reference_tibble,
  reference_cluster_col,
  upsample_cols = where(tof_is_numeric),
  num_neighbors = 1L,
  distance_function = c("euclidean", "cosine", "l2", "ip")
)

Arguments

tof_tibble	A 'tibble' or 'tof_tbl' containing cells to be upsampled into their nearest reference subpopulation.
reference_tibble	A 'tibble' or 'tof_tibble' containing cells that have already been clustered or manually gated into subpopulations.
reference_cluster_col	An unquoted column name indicating which column in 'reference_tibble' contains the subpopulation label (or cluster id) for each cell in 'reference_tibble'.
upsample_cols	Unquoted column names indicating which columns in 'tof_tibble' to use in computing the distances used for upsampling. Defaults to all numeric columns in 'tof_tibble'. Supports tidyselect helpers.
num_neighbors	An integer indicating how many neighbors should be used in the nearest neighbor calculation. Clusters are assigned based on majority vote.
distance_function	A string indicating which distance function should be used to perform the upsampling. Options are "euclidean" (the default) and "cosine".

Value

A tibble with one column named '.upsample_cluster', a character vector of length 'nrow(tof_tibble)' indicating the id of the reference cluster to which each cell (i.e. each row) in 'tof_tibble' was assigned.

Examples

# simulate single-cell data (and reference data with clusters to upsample
# into
sim_data <-
    dplyr::tibble(
        cd45 = rnorm(n = 1000),
        cd38 = rnorm(n = 1000),
        cd34 = rnorm(n = 1000),
        cd19 = rnorm(n = 1000)
    )

reference_data <-
    dplyr::tibble(
        cd45 = rnorm(n = 200),
        cd38 = rnorm(n = 200),
        cd34 = rnorm(n = 200),
        cd19 = rnorm(n = 200),
        cluster_id = c(rep("a", times = 100), rep("b", times = 100))
    )

# upsample using euclidean distance
tof_upsample_neighbor(
    tof_tibble = sim_data,
    reference_tibble = reference_data,
    reference_cluster_col = cluster_id
)

# upsample using cosine distance
tof_upsample_neighbor(
    tof_tibble = sim_data,
    reference_tibble = reference_data,
    reference_cluster_col = cluster_id,
    distance_function = "cosine"
)

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