tests/testthat/test.file.processing.R

In Sconify: A toolkit for performing KNN-based statistics for flow and mass cytometry data

# Date: Jan 20, 2018
# Procedure: test the functions in the process.files script
# Purpose: unit testing for Sconify package

library(Sconify)
library(testthat)
library(magrittr)
library(tibble)
context("Test the file processing arm of the Sconify package")

################ READING IN DATA ################


basal.file <- system.file('extdata',
                      'Bendall_et_al_Cell_Sample_C_basal.fcs',
                      package = "Sconify")

stim.file <- system.file('extdata',
                         'Bendall_et_al_Cell_Sample_C_IL7.fcs',
                         package = "Sconify")

markers.file <- system.file('extdata',
                        'markers.csv',
                        package = "Sconify")

input <- ParseMarkers(markers.file)[[1]]

################ THE TESTING ################

# parse_markers
test_that("Markers csv file is successfully imported", {
    markers <- ParseMarkers(markers.file)
    expect_equal(length(markers), 2)
    expect_equal(length(markers[[1]]), 27)
    expect_equal(length(markers[[2]]), 16)
    expect_equal(names(markers), c("input", "functional"))
    expect_true(is.list(markers))
})

# fcs.to.tibble
test_that("Fcs file gets converted into a tibble data structure", {
    dat <- FcsToTibble(file = basal.file)
    expect_true(is.tibble(dat))
    expect_true(is.data.frame(dat))
    expect_false(is.matrix(dat))
    expect_true(is.atomic(dat[[1]]))
})

test_that("The asinh transform command works", {
    not.tr <- FcsToTibble(file = basal.file, transform = "none")
    tr <- FcsToTibble(file = basal.file)
    tr2 <- FcsToTibble(file = basal.file, transform = "asinh")
    expect_equal(tr[[3]], asinh(not.tr[[3]]/5))
    expect_equal(tr[[3]], tr2[[3]])
})

# Process.multiple.files
test_that("Processing multiple files works on a single file", {
    dat1 <- FcsToTibble(file = basal.file)
    dat2 <- ProcessMultipleFiles(files = basal.file, input = input)
    expect_equal(dat1[,input], dat2[,input])
    expect_equal(length(dat1) + 1, length(dat2))
    expect_equal(length(unique(dat2[["condition"]])), 1)
})

test_that("Process multiple files effectively sub-samples", {
    cell.number <- nrow(FcsToTibble(basal.file))
    testing <- c(cell.number,
                 cell.number %/% 2,
                 cell.number %/% 4,
                 cell.number %/% 8)

    lapply(testing, function(i) {
        curr <- ProcessMultipleFiles(files = basal.file, numcells = i,
                                       input = input)
        expect_equal(nrow(curr), i)
    })

    expect_error(ProcessMultipleFiles(files = basal.file, numcells = 0,
                                        input = input))

    expect_error(ProcessMultipleFiles(files = basal.file, numcells = -3,
                                        input = input))

    expect_error(ProcessMultipleFiles(files = basal.file, numcells = 10.76,
                                        input = input))

    expect_error(ProcessMultipleFiles(files = c(basal.file, stim.file),
                                      numcells = 1,
                                      input = input))
})

test_that("ProcessMultipleFiles divdes contribution of each file equally", {

    testing <- c(100, 99, 2)
    lapply(testing, function(i) {
        dat <- ProcessMultipleFiles(files = basal.file, numcells = 99,
                                      input = input)
        cond.dat <- dat[["condition"]]
        conds <- unique(cond.dat)
        cond1 <- cond.dat[cond.dat == conds[1]]
        cond2 <- cond.dat[cond.dat == conds[2]]
        expect_equal(length(cond1), length(cond2))
    })
})

test_that("Quantile normalization only happens with two or more files", {
    expect_error(process.multiple.files(basal.file,
                                        input = input,
                                        norm = TRUE))
})

# Quantile normalization testing
test_that("Simple quantile normalization case", {
    dat <- list(tibble(v1 = 1:10), tibble(v1 = 11:20))
    q.dat <- QuantNormalizeElements(dat)
    expect_equal(q.dat[[1]], q.dat[[2]])

    dat <- list(tibble(v1 = 1:5), tibble(v2 = 2, 4, 6, 8, 10))
    q.dat <- QuantNormalizeElements(dat)
    expect_equal(q.dat[[1]], q.dat[[2]])

    dat <- list(tibble(v1 = c(1, 3, 5, 7)), tibble(v2 = c(2, 4, 6, 8)))
    q.dat <- QuantNormalizeElements(dat)
    expect_equal(q.dat[[1]], q.dat[[2]])
})

# Split file
test_that("Split file returns two conditions", {
    dat <- SplitFile(basal.file, numcells = 10000, input.markers = input)
    expect_equal(length(unique(dat$condition)), 2)
})

test_that("Split file can only be run on a single file", {
    expect_error(SplitFile(c(basal.file, stim.file),
                           numcells = 10000,
                           input.markers = input))
})

test_that("Split file handles an odd number of cells", {
    dat <- SplitFile(basal.file, numcells = 99, input.markers = input)
    expect_equal(nrow(dat), 98)
})