tests/testthat/test.post.processing.R

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

# Date: January 28, 2018
# Procedure: testing the post processing function
# Purpose: unit testing for the testthat package
library(testthat)
library(Sconify)
context("Test the post processing functions for the Sconify package")

test_that("Subsampling and tSNE functionality works", {
    test.tsne <- SubsampleAndTsne(wand.combined, input.markers, 100)
    expect_equal(ncol(test.tsne), ncol(wand.combined) + 2)
    expect_equal(length(grep("bh-SNE", colnames(test.tsne))), 2)
})

test_that("String to numbers works", {
    test.str <- StringToNumbers(c("hi", "hi", "bye", "hi"))
    expect_equal(test.str, c(1, 1, 2, 1))
})


test_that("Basic post-processing functionality", {
    test.pp <- PostProcessing(scone.output = wand.scone,
                              cell.data = wand.combined,
                              input = input.markers,
                              tsne = TRUE,
                              log.transform.qvalue = TRUE)
    expect_equal(ncol(test.pp), ncol(wand.final))
})

test_that("Log transforming q values works", {
    test.pp <- PostProcessing(scone.output = wand.scone,
                              cell.data = wand.combined,
                              input = input.markers,
                              tsne = FALSE,
                              log.transform.qvalue = FALSE)
    q <- test.pp[grep("qvalue", names(test.pp))]
    expect_true(all(q <= 1))

    test.ppq <- PostProcessing(scone.output = wand.scone,
                              cell.data = wand.combined,
                              input = input.markers,
                              tsne = FALSE,
                              log.transform.qvalue = TRUE)

    expect_false(all(test.pp == test.ppq))
    expect_true(max(test.ppq) > 1)
})

test_that("Edge cases for the tSNE vis function", {
    expect_error(TsneVis(final = wand.final, marker = "test", label = "test"))
})

test_that("Testing the output of the tSNE vis function", {
    expect_type(TsneVis(final = wand.final,
                        marker = "pSTAT5(Nd150)Di.IL7.change",
                        label = "test"),
                "list")
})

test_that("Testing the output of the make.hist function", {
    expect_type(MakeHist(wand.final,
                         100,
                         "IL7.fraction.cond.2",
                         "fraction IL7"),
                "list")
})