tests/testthat/test_290splicing.R

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

start <- as.POSIXlt(Sys.time())
library(hpgldata)
context("290alt_splicing.R:\n")

mtb_rmats_untarred <- utils::untar(tarfile = system.file("share/mtb_rmats.tar.xz",
                                                         package = "hpgldata"))

basedir <- "mtb_rmats/rmats_hg38_91"
## Define the prefixes
skipped_exon <- "SE"
alt_5p_splice_site <- "A5SS"
alt_3p_splice_site <- "A3SS"
mutually_exclusive <- "MXE"
retained_introns <- "RI"

## Define the suffixes
## Described in the documentation as 'with only reads that span splicing
## junctions'.
spanning_suffix <- ".MATS.JC.txt"
## Described in the documentation as 'with reads that span splicing junctions
## and reads on target (striped regions in the home page figure.)."
both_suffix <- ".MATS.JCEC.txt"

spanning_a3ss <- file.path(basedir, paste0(alt_3p_splice_site, spanning_suffix))
both_a3ss <- file.path(basedir, paste0(alt_3p_splice_site, both_suffix))
spanning_a5ss <- file.path(basedir, paste0(alt_5p_splice_site, spanning_suffix))
both_a5ss <- file.path(basedir, paste0(alt_5p_splice_site, both_suffix))
spanning_mxe <- file.path(basedir, paste0(mutually_exclusive, spanning_suffix))
both_mxe <- file.path(basedir, paste0(mutually_exclusive, both_suffix))
spanning_se <- file.path(basedir, paste0(skipped_exon, spanning_suffix))
both_se <- file.path(basedir, paste0(skipped_exon, both_suffix))
spanning_ri <- file.path(basedir, paste0(retained_introns, spanning_suffix))
both_ri <- file.path(basedir, paste0(retained_introns, both_suffix))

rmats_plots <- plot_rmats(
  se = both_se, a5ss = both_a5ss, a3ss = both_a3ss,
  mxe = both_mxe, ri = both_ri)

expected <- "gg"
actual <- class(rmats_plots[["ma"]])[1]
test_that("We get a plot of some rMATS data?", {
  expect_equal(expected, actual)
})

## I changed my suppa invocation and plotter pretty significantly.
## I neeed therefore to grab a new copy of these dpsi/tpm/etc files.
##suppa_rmats_untarred <- utils::untar(tarfile = system.file("share/mtb_suppa.tar.xz",
##                                                           package = "hpgldata"))
##basedir <- "mtb_suppa/preprocessing/outputs/suppa_hg38_91"
##dpsi_file <- file.path(basedir, "uninf_inf_diffsplice.dpsi")
##tpm_file <- file.path(basedir, "uninf_inf_diffsplice_avglogtpm.tab")
##events_file <- file.path(basedir, "ensembl_hg38.events.ioe")
##psi_file <- file.path(basedir, "uninf_inf_diffsplice.psivec")
##
##suppa_plots <- plot_suppa(dpsi_file, tpm_file,
##                          events = events_file,
##                          label_type = "Skipping exon",
##                          psi = psi_file)
##actual <- class(suppa_plots[["ma"]])[1]
##test_that("We get a plot of some suppa data?", {
##  expect_equal(expected, actual)
##})
##
## annotation <- load_biomart_annotations()[["annotation"]]
##stuff <- write_suppa_table(suppa_plots[["data"]], excel = "suppa.xlsx",
##                           annotations = NULL)
##actual <- nrow(stuff)
##expected <- 72000
##test_that("Can we write out suppa data?", {
##  expect_gt(actual, expected)
##})
##removed <- file.remove("suppa.xlsx")

end <- as.POSIXlt(Sys.time())
elapsed <- round(x = as.numeric(end - start))
message("\nFinished 290alt_splicing.R in ", elapsed,  " seconds.")