tests/testthat/test_plot2D.R

In pRoloc: A unifying bioinformatics framework for spatial proteomics

## context("plot2D using visualTest")
## reference figures are in inst/figs/.
## library("visualTest")

## see https://github.com/MangoTheCat/visualTest/issues/19
## thr <- ifelse(Sys.info()[["nodename"]] == "elyacin", 1e-3, 25)

## test_that("Negative control", {
##     expect_false(
##         isSimilar(system.file("figs/plot2D-null-black.png", package = "pRoloc"),
##                   system.file("figs/plot2D-null.png", package = "pRoloc"),
##                   threshold = thr))
##     expect_false(
##         isSimilar(system.file("figs/plot2D-null-black.png", package = "pRoloc"),
##                   system.file("figs/plot2D.png", package = "pRoloc"),
##                   threshold = thr))
## })

## test_that("Positive control", {
##     expect_true(
##         isSimilar(system.file("figs/plot2D-null.png", package = "pRoloc"),
##                   system.file("figs/plot2D-null.png", package = "pRoloc"),
##                   threshold = thr))
##     expect_true(
##         isSimilar(system.file("figs/plot2D.png", package = "pRoloc"),
##                   system.file("figs/plot2D.png", package = "pRoloc"),
##                   threshold = thr))
## })

## test_that("plot2D(hyperLOPIT2015, fcol = NULL)", {
##     ref <- system.file("figs/plot2D-null.png", package = "pRoloc")
##     data(hyperLOPIT2015)   
##     tmpf <- paste0(tempfile(), ".png")
##     png(tmpf)
##     plot2D(hyperLOPIT2015, fcol = NULL)
##     dev.off()
##     expect_true(isSimilar(tmpf, ref, threshold = thr))
##     unlink(tmpf)
## })

## test_that("plot2D(hyperLOPIT2015, fcol = NULL, col = 'black')", {
##     ref <- system.file("figs/plot2D-null-black.png", package = "pRoloc")
##     data(hyperLOPIT2015)
##     tmpf <- paste0(tempfile(), ".png")
##     png(tmpf)
##     plot2D(hyperLOPIT2015, fcol = NULL, col = "black")
##     dev.off()
##     expect_true(isSimilar(tmpf, ref, threshold = thr))
##     unlink(tmpf)
## })

## test_that("plot2D(hyperLOPIT2015)", {
##     ref <- system.file("figs/plot2D.png", package = "pRoloc")
##     data(hyperLOPIT2015)
##     tmpf <- paste0(tempfile(), ".png")
##     png(tmpf)
##     plot2D(hyperLOPIT2015)
##     dev.off()
##     expect_true(isSimilar(tmpf, ref))
##     unlink(tmpf)
## })

## test_that("plot2D(hyperLOPIT2015, fcol = NULL, cex = 3)", {
##     ref <- system.file("figs/plot2D-null-cex.png", package = "pRoloc")
##     data(hyperLOPIT2015)
##     tmpf <- paste0(tempfile(), ".png")
##     png(tmpf)
##     plot2D(hyperLOPIT2015, fcol = NULL, cex = 3)
##     dev.off()
##     expect_true(isSimilar(tmpf, ref, threshold = thr))
##     unlink(tmpf)
## })

## test_that("plot2D(hyperLOPIT2015, fcol = NULL, pch = 3)", {
##     data(hyperLOPIT2015)
##     tmpf <- paste0(tempfile(), ".png")
##     png(tmpf)
##     plot2D(hyperLOPIT2015, fcol = NULL, pch = 3)
##     dev.off()
##     expect_true(isSimilar(tmpf,
##                           system.file("figs/plot2D-null-pch.png", package = "pRoloc"),
##                           threshold = thr))
##     unlink(tmpf)
## })

## test_that("plot2D(hyperLOPIT2015, fcol = NULL, pch = 19, col = 'black')", {
##     ref <- system.file("figs/plot2D-null-pch-black.png", package = "pRoloc")
##     data(hyperLOPIT2015)
##     tmpf <- paste0(tempfile(), ".png")
##     png(tmpf)
##     plot2D(hyperLOPIT2015, fcol = NULL, pch = 19, col = "black")
##     dev.off()
##     expect_true(isSimilar(tmpf, ref, threshold = thr))
##     unlink(tmpf)
## })

## test_that("plot2D(hyperLOPIT2015, method = 'scree')", {
##     data(hyperLOPIT2015)
##     tmpf <- paste0(tempfile(), ".png")
##     png(tmpf)
##     plot2D(hyperLOPIT2015, method = "scree")
##     dev.off()
##     expect_true(isSimilar(tmpf,
##                           system.file("figs/plot2D-scree.png", package = "pRoloc"),
##                           threshold = thr))
##     unlink(tmpf)
## })

## test_that("plot2D(hyperLOPIT2015, method = 'hexbin')", {
##     ref <- system.file("figs/plot2D-hexbin.png", package = "pRoloc")
##     data(hyperLOPIT2015)
##     tmpf <- paste0(tempfile(), ".png")
##     png(tmpf)
##     plot2D(hyperLOPIT2015, method = "hexbin")
##     dev.off()
##     expect_true(isSimilar(tmpf, ref, threshold = thr))
##     unlink(tmpf)
## })

## test_that("plot2D(hyperLOPIT2015, method = 'lda')", {
##     ref <- system.file("figs/plot2D-lda.png", package = "pRoloc")
##     data(hyperLOPIT2015)
##     tmpf <- paste0(tempfile(), ".png")
##     png(tmpf)
##     plot2D(hyperLOPIT2015, method = "lda")
##     dev.off()
##     expect_true(isSimilar(tmpf, ref, threshold = thr))
##     unlink(tmpf)
## })

test_that("plot2D(, method = 't-SNE') with duplicated feature", {
    library("pRolocdata")
    data("E14TG2aS1")
    ## Q1HFZ0 Q99LX0 
    ## 630    894
    ## are identical    
    x <- E14TG2aS1[c(600:850,880:900), ]
    expect_message(tsne <- plot2D(x, method = "t-SNE", plot = FALSE),
                   "Only keeping unique features, dropped 1.")
    expect_identical(nrow(x) - nrow(tsne), 1L)
})