tests/testthat/test-workflow.R

In IrisSpatialFeatures: A package to extract spatial features based on multiplex IF images

context("workflow")
test_that("steps of a workflow excute", {
    # Test read_raw
    raw_data <- read_raw(path=system.file("extdata", package = "IrisSpatialFeatures"),
                        format='Mantra')
    expect_equal(length(raw_data@markers),3)
    # Test threshold_dataset
    dataset <- threshold_dataset(raw_data,
                                 marker='PD-Ligand-1 (Opal 690)',
                                 marker_name='PDL1',
                                 base=c('SOX10+'))
    dataset <- threshold_dataset(dataset,
                                 marker='PD-1 (Opal 540)',
                                 marker_name='PD1',
                                 base=c('CD8+','OTHER'))

    expect_equal(length(dataset@markers),6)
})