tests/testthat/test_061se.R

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

start <- as.POSIXlt(Sys.time())
library(hpgldata)

context("061se.R")
## Functions exported in expt.r
## make_pombe_expt(), create_expt(), concatenate_runs(), exclude_genes_expt(),
## features_greater_than(), make_exampledata(), median_by_factor(),
## set_expt_batches(), set_expt_colors(), set_expt_conditions(),
## set_expt_factors(), set_expt_samplenames(), subset_expt(), what_happened(),
## write_expt()
## S4 methods: exprs(), fData(), pData(), notes()

## make_pombe_expt() invokes create_expt()
pombe_se <- make_pombe_se()
chosen_genes <- c("SPAC212.11", "SPAC212.09c", "SPNCRNA.70",
                  "SPAC212.12", "SPAC212.04c", "SPAC212.03",
                  "SPAC212.02", "SPAC212.01c", "SPAC977.03")

## fData()
testing <- fData(pombe_se)
actual <- dim(testing)
expected <- c(7039, 10)
## 0102
test_that("Do we get annotation data from our expt?", {
  expect_equal(actual[1], expected[1])
  expect_equal(actual[2], expected[2])
})
actual <- testing[chosen_genes, "start_position"]
expected <- c("1", "7619", "11027", "15855", "21381",
              "23589", "27353", "28738", "33835")
## 03
test_that("Do we get annotation data from our expt?", {
  expect_equal(actual, expected)
})

## pData()
testing <- pData(pombe_se)
actual <- dim(testing)
expected <- c(36, 7)
## 0405
test_that("Do we get experimental metadata from our expt?", {
  expect_equal(actual[1], expected[1])
  expect_equal(actual[2], expected[2])
})

## exprs()
testing <- exprs(pombe_se)
actual <- dim(testing)
expected <- c(7039, 36)
## 0607
test_that("Do we get expression from our expt?", {
  expect_equal(actual[1], expected[1])
  expect_equal(actual[2], expected[2])
})
## Check that the number distribution is what we expect
actual <- as.numeric(summary(testing[, 1]))
expected <- c(0.000, 46.000, 306.000, 2225.509, 869.000, 4542884.000)
## 13
test_that("Do we get expression from our expt?", {
  expect_equal(actual[1], expected[1], tolerance = 0.001)
  expect_equal(actual[2], expected[2], tolerance = 0.001)
  expect_equal(actual[3], expected[3], tolerance = 0.001)
  expect_equal(actual[4], expected[4], tolerance = 0.001)
  expect_equal(actual[5], expected[5], tolerance = 0.001)
  expect_equal(actual[6], expected[6], tolerance = 0.001)
})

## concatenate_runs()
##test_expt <- concatenate_runs(expt = pombe_se, column = "minute")
##actual <- dim(pData(test_expt))
##expected <- c(6, 8)
##test_that("Do we get a reasonable number of resulting samples if we collapse by time?", {
##  expect_equal(actual[1], expected[1], tolerance = 0.001)
##  expect_equal(actual[2], expected[2], tolerance = 0.001)
##})

## exclude_genes_expt()
##no_rrna <- exclude_genes_expt(pombe_se,
##                              column = "gene_biotype",
##                              patterns = c("ncRNA", "pseudogene"))
##expected <- 5778
##actual <- nrow(exprs(no_rrna))
#### 16
##test_that("Does exclude_genes_expt remove stuff?", {
##  expect_equal(actual, expected)
##})

## features_greater_than()
testing_1 <- features_greater_than(pombe_se, cutoff = 1, hard = FALSE)
testing_10 <- features_greater_than(pombe_se, cutoff = 10, hard = FALSE)
testing_100 <- features_greater_than(pombe_se, cutoff = 100, hard = FALSE)
testing_1000 <- features_greater_than(pombe_se, cutoff = 1000, hard = FALSE)
testing_10000 <- features_greater_than(pombe_se, cutoff = 10000, hard = FALSE)
testing_100000 <- features_greater_than(pombe_se, cutoff = 100000, hard = FALSE)
## 22
test_that("Do we get expected features greater than some cutoffs?", {
  expect_equal(as.numeric(testing_1[["number"]][1]), 6457)
  expect_equal(as.numeric(testing_10[["number"]][1]), 5974)
  expect_equal(as.numeric(testing_100[["number"]][1]), 4754)
  expect_equal(as.numeric(testing_1000[["number"]][1]), 1566)
  expect_equal(as.numeric(testing_10000[["number"]][1]), 212)
  expect_equal(as.numeric(testing_100000[["number"]][1]), 5)
})

## median_by_factor()
## I changed the output of this function!
medians <- median_by_factor(pombe_se)[["medians"]]
actual <- medians[chosen_genes, 1]
expected <- c(7, 41, 0, 0, 43, 0, 0, 2, 0)
test_that("Do we get expected medians?", {
  expect_equal(expected, actual)
})

## set_expt_batches()
##new_batches <- c(rep(x = "a", times = 12), rep(x = "b", times = 12), rep(x = "c", times = 12))
##testing <- set_expt_batches(pombe_se, fact = new_batches)
##actual <- pData(testing)[["batch"]]
## 26
##test_that("Did we change the batches?", {
##  expect_equal(new_batches, actual)
##})

## set_expt_colors()
testing <- set_expt_colors(pombe_se, chosen_palette = "Accent")
new_actual <- levels(as.factor(testing$colors))
new_expected <- c("#5C86AB", "#666666", "#7FC97F", "#8B3B99", "#9E5F33", "#A7B7B5",
                  "#CC4233", "#CFB2BE", "#DAE49D", "#EB0A75", "#F7BE8D", "#FEE290")
test_that("Did we get some old/new colors?", {
  expect_equal(new_actual, new_expected)
})

## set_expt_conditions()
##testing <- set_expt_conditions(pombe_se, fact = "minute")
##expected <- levels(pombe_se[["design"]][["minute"]])
##actual <- levels(testing[["design"]][["condition"]])
##test_that("Did we get some new conditions?", {
##  expect_equal(actual, expected)
##})

## set_expt_factors()
## This function just calls set_expt_batches and set_expt_conditions.  I am not testing it.

## set_expt_samplenames()
##newnames <- paste0(sampleNames(pombe_se), "test")
##testing <- set_expt_samplenames(pombe_se, newnames = newnames)
##test_that("Can we change the same names?", {
##  expect_equal(newnames, sampleNames(testing))
##})

## subset_expt()
##testing <- subset_expt(pombe_se, subset = "replicate=='r1'")
##actual <- sampleNames(testing)
##expected <- c("GSM1368273", "GSM1368276", "GSM1368279", "GSM1368282",
##              "GSM1368285", "GSM1368288", "GSM1368291", "GSM1368294",
##              "GSM1368297", "GSM1368300", "GSM1368303", "GSM1368306")
##test_that("Can we subset an expt?", {
##  expect_equal(expected, actual)
##})

## what_happened()
##testing <- normalize_expt(pombe_se, transform = "log2", norm = "tmm",
##                          convert = "cpm", filter = TRUE, batch = "sva")
##actual <- what_happened(testing)
##expected <- glue::glue("log2(sva(cpm(tmm(cbcb(data)))))")
##test_that("Will an expt tell us what happened to it?", {
##  expect_equal(expected, actual)
##})

## write_expt()
## I run this on an interactive session and get no warnings...
##testing <- sm(write_expt(pombe_se, excel = "testing_write_expt.xlsx"))
##test_that("Did write_expt() work?", {
##  expect_true(file.exists("testing_write_expt.xlsx"))
##})
##tt <- file.remove("testing_write_expt.xlsx")

test <- plot_libsize(pombe_se)

end <- as.POSIXlt(Sys.time())
elapsed <- round(x = as.numeric(end - start))
message("\nFinished 060expt.R in ", elapsed,  " seconds.")