tof_estimate_density: Estimate the local densities for all cells in a...

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

Estimate the local densities for all cells in a high-dimensional cytometry dataset.

Description

This function is a wrapper around tidytof's tof_*_density() function family. It performs local density estimation on high-dimensional cytometry data using a user-specified method (of 3 choices) and each method's corresponding input parameters.

Usage

tof_estimate_density(
  tof_tibble,
  distance_cols = where(tof_is_numeric),
  distance_function = c("euclidean", "cosine", "l2", "ip"),
  normalize = TRUE,
  ...,
  augment = TRUE,
  method = c("mean_distance", "sum_distance", "spade")
)

Arguments

tof_tibble	A 'tof_tbl' or a 'tibble'.
distance_cols	Unquoted names of the columns in 'tof_tibble' to use in calculating cell-to-cell distances during the local density estimation for each cell. Defaults to all numeric columns in 'tof_tibble'.
distance_function	A string indicating which distance function to use for calculating cell-to-cell distances during local density estimation. Options include "euclidean" (the default) and "cosine".
normalize	A boolean value indicating if the vector of local density estimates should be normalized to values between 0 and 1. Defaults to TRUE.
...	Additional arguments to pass to the 'tof_*_density()' function family member corresponding to the chosen 'method'.
augment	A boolean value indicating if the output should column-bind the local density estimates of each cell as a new column in 'tof_tibble' (TRUE; the default) or if a single-column tibble including only the local density estimates should be returned (FALSE).
method	A string indicating which local density estimation method should be used. Valid values include "mean_distance", "sum_distance", and "spade".

Value

A 'tof_tbl' or 'tibble' If augment = FALSE, it will have a single column encoding the local density estimates 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 local density estimates.

See Also

Other local density estimation functions: tof_knn_density(), tof_spade_density()

Examples

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

# perform the density estimation
tof_estimate_density(tof_tibble = sim_data, method = "spade")

# perform the density estimation with a smaller search radius around
# each cell
tof_estimate_density(
    tof_tibble = sim_data,
    alpha_multiplier = 2,
    method = "spade"
)

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