stratify: Stratify operations.

In cytomining/cytominer: Methods for Image-Based Cell Profiling

Stratify operations.

Description

stratify stratifies operations.

Usage

stratify(population, sample, reducer, strata, ...)

Arguments

population	tbl with grouping (metadata) and observation variables.
sample	tbl with the same structure as population. This is typically used by operations to estimate parameters.
reducer	operation that is to applied in a stratified manner.
strata	optional character vector specifying grouping variables for stratification.
...	arguments passed to operation.

Value

population with potentially extra columns.

Examples

suppressMessages(suppressWarnings(library(magrittr)))
population <- tibble::tibble(
  Metadata_group = sample(c("a", "b"), 100, replace = TRUE),
  Metadata_type = sample(c("control", "trt"), 100, replace = TRUE),
  AreaShape_Area = c(rnorm(98), 20, 30),
  AreaShape_Eccentricity = rnorm(100)
)
variables <- c("AreaShape_Area", "AreaShape_Eccentricity")
strata <- c("Metadata_group")
sample <- population %>% dplyr::filter(Metadata_type == "control")
population_marked <-
  cytominer::stratify(
    reducer = cytominer::mark_outlier_rows,
    method = "svd+iqr",
    population = population,
    variables = variables,
    sample = sample,
    strata = strata
  )
population_marked %>%
  dplyr::group_by(is_outlier) %>%
  dplyr::sample_n(3)

cytomining/cytominer documentation built on July 5, 2023, 3:34 a.m.