tof_downsample: Downsample high-dimensional cytometry data.

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

Downsample high-dimensional cytometry data.

Description

This function downsamples the number of cells in a 'tof_tbl' using the one of three methods (randomly sampling a constant number of cells, randomly sampling a proportion of cells, or performing density-dependent downsampling per the algorithm in Qiu et al., (2011)).

Usage

tof_downsample(
  tof_tibble,
  group_cols = NULL,
  ...,
  method = c("constant", "prop", "density")
)

Arguments

tof_tibble	A 'tof_tbl' or a 'tibble'.
group_cols	Unquoted names of the columns in 'tof_tibble' that should be used to define groups within which the downsampling will be performed. Supports tidyselect helpers. Defaults to 'NULL' (no grouping).
...	Additional arguments to pass to the 'tof_downsample_*' function family member corresponding to the chosen method.
method	A string indicating which downsampling method to use: "constant" (the default), "prop", or "density".

Value

A downsampled 'tof_tbl' with the same number of columns as the input 'tof_tibble', but fewer rows. The number of rows in the result will depend on the chosen downsampling method.

See Also

Other downsampling functions: tof_downsample_constant(), tof_downsample_density(), tof_downsample_prop()

Examples

sim_data <-
    dplyr::tibble(
        cd45 = rnorm(n = 1000),
        cd38 = rnorm(n = 1000),
        cd34 = rnorm(n = 1000),
        cd19 = rnorm(n = 1000),
        cluster_id = sample(letters, size = 1000, replace = TRUE)
    )

# sample 200 cells from the input data
tof_downsample(
    tof_tibble = sim_data,
    num_cells = 200L,
    method = "constant"
)

# sample 10% of all cells from the input data
tof_downsample(
    tof_tibble = sim_data,
    prop_cells = 0.1,
    method = "prop"
)

# sample ~10% of cells from the input data using density dependence
tof_downsample(
    tof_tibble = sim_data,
    target_prop_cells = 0.1,
    method = "density"
)

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