tests/testthat/test-coord_geo.R

In willgearty/deeptime: Plotting Tools for Anyone Working in Deep Time

test_that("coord_geo works", {
  skip_if_not_installed("divDyn")
  gg <- ggplot(coral_div) +
    geom_line(aes(x = stage_age, y = n)) +
    scale_x_reverse("Age (Ma)") +
    ylab("Coral Genera") +
    coord_geo(xlim = c(250, 0), ylim = c(0, 1700)) +
    theme_classic()
  expect_true(is(ggplot_build(gg)$layout$coord, "CoordGeo"))
  expect_equal(ggplot_build(gg)$layout$panel_params[[1]]$x.range, c(-250, 0))
  gg <- ggplot(coral_div) +
    geom_line(aes(x = stage_age, y = n)) +
    scale_x_continuous("Age (Ma)") +
    ylab("Coral Genera") +
    coord_geo(xlim = c(250, 0), ylim = c(10, 1700), ytrans = "log10") +
    theme_classic()
  expect_true(is.ggplot(gg))
  params <- ggplot_build(gg)$layout$panel_params[[1]]
  expect_equal(params$x.range, c(0, 250))
  expect_equal(params$y.range, c(log10(10), log10(1700)))
  expect_error({
    ggplot(coral_div) +
      geom_line(aes(x = stage_age, y = n)) +
      coord_geo(xlim = c(250, 0), ylim = c(10, 1700), xtrans = 5)
  })
  expect_error({
    ggplot(coral_div) +
      geom_line(aes(x = stage_age, y = n)) +
      coord_geo(xlim = c(250, 0), ylim = c(10, 1700),
                ytrans = list(x = 5, y = 2))
  })
  gg <- ggplot(coral_div) +
    geom_line(aes(x = stage_age, y = n)) +
    coord_geo(xlim = c(250, 0), ylim = c(10, 1700), height = 5)
  expect_error(plot(gg))
  gg <- ggplot(coral_div) +
    geom_line(aes(x = stage_age, y = n)) +
    coord_geo(dat = 5, xlim = c(250, 0), ylim = c(10, 1700))
  expect_error(plot(gg))
  gg <- ggplot(coral_div) +
    geom_line(aes(x = stage_age, y = n)) +
    coord_geo(xlim = c(250, 0), ylim = c(10, 1700), size = "big")
  expect_error(plot(gg))
  expect_error({
    ggplot(coral_div) +
      geom_line(aes(x = stage_age, y = n)) +
      coord_geo(pos = "middle", xlim = c(250, 0), ylim = c(10, 1700))
  })
})

test_that("stacking scales works", {
  skip_if_not_installed("divDyn")
  gg <- ggplot(coral_div) +
    geom_line(aes(x = stage_age, y = n)) +
    scale_x_reverse("Age (Ma)") +
    ylab("Coral Genera") +
    coord_geo(
      dat = list("periods", "eras"), xlim = c(250, 0), ylim = c(0, 1700),
      pos = list("b", "b"), abbrv = list(TRUE, FALSE)
    ) +
    theme_classic()
  expect_doppelganger_deeptime("stacked scales", gg)
})

test_that("scales on different sides works", {
  skip_if_offline(host = "macrostrat.org")
  skip_if_not_installed("gsloid")
  gg <- ggplot(lisiecki2005) +
    geom_line(aes(x = d18O, y = Time / 1000), orientation = "y") +
    scale_y_reverse("Time (Ma)", sec.axis = sec_axis(~.)) +
    coord_geo(dat = list("Geomagnetic Polarity Chron",
                         "Planktic foraminiferal Primary Biozones"),
              xlim = c(2, 6), ylim = c(5.5, 0), pos = list("l", "r"), rot = 90,
              skip = "PL4", size = list(5, 4), xtrans = "sqrt") +
    theme_classic()
  expect_doppelganger_deeptime("scales on different sides1", gg)
  gg <- ggplot(lisiecki2005) +
    geom_line(aes(y = d18O, x = Time / 1000), orientation = "x") +
    scale_x_reverse("Time (Ma)", sec.axis = sec_axis(~.)) +
    coord_geo(dat = list("Geomagnetic Polarity Chron",
                         "Planktic foraminiferal Primary Biozones"),
              ylim = c(2, 6), xlim = c(5.5, 0), pos = list("t", "b"),
              skip = "PL4", size = list(5, 4), ytrans = "log10") +
    theme_classic()
  expect_doppelganger_deeptime("scales on different sides2", gg)
})

test_that("scales on facetted plot works", {
  skip_if_not_installed("divDyn")
  gg <- ggplot(coral_div_diet) +
    geom_line(aes(x = stage_age, y = n)) +
    scale_x_reverse("Age (Ma)") +
    ylab("Coral Genera") +
    coord_geo(xlim = c(250, 0)) +
    theme_classic()
  expect_doppelganger_deeptime("scale on only one facet",
                               gg + facet_wrap(~diet, nrow = 3))
  expect_doppelganger_deeptime("scale on all facets",
                               gg +
                                 facet_wrap(~diet, nrow = 3, scales = "free_x"))
})

test_that("auto-discrete scale works", {
  skip_if_not_installed("divDyn")
  gg <- ggplot(coral_div_dis) +
    geom_col(aes(x = period, y = n, fill = diet)) +
    scale_x_discrete("Period", limits = unique(coral_div_dis$period),
                     labels = NULL, expand = expansion(add = .5)) +
    scale_y_continuous(expand = c(0, 0)) +
    scale_fill_viridis_d() +
    ylab("Coral Genera") +
    coord_geo(expand = TRUE, skip = NULL, abbrv = FALSE) +
    theme_classic() +
    theme(axis.ticks.length.x = unit(0, "lines"))
  expect_doppelganger_deeptime("scale on discrete axis", gg)
})

test_that("custom discrete scale works", {
  skip_if_not_installed("divDyn")
  eras_custom <- data.frame(name = c("Mesozoic", "Cenozoic"),
                            max_age = c(0.5, 3.5), min_age = c(3.5, 6.5),
                            color = c("#67C5CA", "#F2F91D"))

  gg <- ggplot(coral_div_dis) +
    geom_col(aes(x = period, y = n, fill = diet)) +
    scale_x_discrete(NULL, limits = unique(coral_div_dis$period),
                     labels = NULL, expand = expansion(add = .5)) +
    scale_y_continuous(expand = c(0, 0)) +
    scale_fill_viridis_d() +
    ylab("Coral Genera") +
    coord_geo(dat = list("periods", eras_custom), pos = c("b", "b"),
              expand = TRUE, skip = NULL, abbrv = FALSE,
              dat_is_discrete = list(FALSE, TRUE)) +
    theme_classic() +
    theme(axis.ticks.length.x = unit(0, "lines"))
  expect_doppelganger_deeptime("custom discrete scale", gg)
})

test_that("geom_fit_text() works", {
  skip_if_not_installed("divDyn")
  gg <- ggplot(coral_div) +
    geom_line(aes(x = stage_age, y = n)) +
    scale_x_reverse("Age (Ma)") +
    ylab("Coral Genera") +
    coord_geo(dat = "periods", xlim = c(250, 0), ylim = c(0, 1700),
      abbrv = FALSE, size = "auto", fittext_args = list(size = 20)) +
    theme_classic()
  expect_doppelganger_deeptime("geom_fit_text()", gg)
  gg <- ggplot(coral_div) +
    geom_line(aes(x = stage_age, y = n)) +
    coord_geo(dat = "periods", xlim = c(250, 0), ylim = c(0, 1700),
              abbrv = FALSE, size = "auto", fittext_args = 20)
  expect_error(plot(gg))
})

test_that("ggtree scale works", {
  skip_if_not_installed("ggtree")
  skip_if_not_installed("phytools")
  gg <- ggtree(mammal.tree) +
    coord_geo(xlim = c(-75, 0), ylim = c(-2, Ntip(mammal.tree)),
              neg = TRUE, abbrv = FALSE) +
    scale_x_continuous(breaks = seq(-80, 0, 20),
                       labels = abs(seq(-80, 0, 20))) +
    theme_tree2()
  expect_doppelganger_deeptime("scale on ggtree", revts(gg))
})

test_that("ggtree scale works with only fossil taxa", {
  skip_if_not_installed("ggtree")
  skip_if_not_installed("paleotree")
  gg <- ggtree(ceratopsianTreeRaia,
               position = position_nudge(x = -ceratopsianTreeRaia$root.time)) +
    coord_geo(xlim = c(-163.5, -50), ylim = c(-2, Ntip(ceratopsianTreeRaia)),
      pos = list("bottom", "bottom"), skip = c("Paleocene", "Middle Jurassic"),
      dat = list("epochs", "periods"), abbrv = FALSE,
      size = list(4, 5), neg = TRUE, center_end_labels = TRUE) +
    scale_x_continuous(breaks = -rev(epochs$max_age),
                       labels = rev(epochs$max_age)) +
    theme_tree2() +
    theme(plot.margin = margin(7, 11, 7, 11))
  expect_doppelganger_deeptime("scale on fossil ggtree", gg)
})