Nothing
skip_if_not_installed("ggtree")
test_that("coord_geo_polar works", {
skip_if_not_installed("ape")
lifecycle::expect_deprecated({
gg <- revts(ggtree(tree)) +
coord_geo_polar(dat = "stages") +
scale_x_continuous(limits = c(NA, 0))
})
expect_true(is.ggplot(gg))
expect_true(is(ggplot_build(gg)$layout$coord, "CoordGeoPolar"))
expect_doppelganger_deeptime("coord_geo_polar", gg)
expect_equal(ggplot_build(gg)$layout$panel_params[[1]]$r.range,
c(-max(node.depth.edgelength(tree)), 0))
withr::local_options(lifecycle_verbosity = "quiet")
gg2 <- revts(ggtree(tree)) +
coord_geo_polar(dat = "stages", fill = c("grey60", "grey80")) +
scale_x_continuous(limits = c(NA, 0))
expect_true(is.ggplot(gg2))
expect_true(is(ggplot_build(gg2)$layout$coord, "CoordGeoPolar"))
expect_doppelganger_deeptime("coord_geo_polar_grey", gg2)
# this doesn't make sense, but let's test it anyways
gg3 <- ggtree(tree) +
coord_geo_polar(dat = "stages", neg = FALSE) +
scale_x_continuous(limits = c(0, NA))
expect_true(is.ggplot(gg3))
expect_true(is(ggplot_build(gg3)$layout$coord, "CoordGeoPolar"))
expect_doppelganger_deeptime("coord_geo_polar_pos", gg3)
expect_equal(ggplot_build(gg3)$layout$panel_params[[1]]$r.range,
c(0, max(node.depth.edgelength(tree))))
expect_error({
ggtree(tree) +
coord_geo_polar(direction = "up")
})
gg4 <- ggtree(tree) +
coord_geo_polar(dat = 5)
expect_error(plot(gg4))
})
test_that("stacking scales works", {
withr::local_options(lifecycle_verbosity = "quiet")
skip_if_not_installed("phytools")
gg <- revts(ggtree(mammal.tree)) +
coord_geo_polar(
dat = list("stages", "periods"), alpha = .5,
prop = list(0.75, .25), start = pi / 4, lty = "dashed"
) +
scale_y_continuous(expand = expansion(mult = c(0.02, 0.02))) +
theme(deeptime.axis.text.r = element_text(size = 3.5, hjust = .25,
vjust = .75))
expect_doppelganger_deeptime("stacked scales", gg)
})
test_that("ggtree scale works with only fossil taxa", {
withr::local_options(lifecycle_verbosity = "quiet")
skip_if_not_installed("paleotree")
skip_if_not_installed("geomtextpath")
gg <- ggtree(ceratopsianTreeRaia,
position = position_nudge(
x = -ceratopsianTreeRaia$root.time
)) +
coord_geo_polar(dat = "stages")
expect_doppelganger_deeptime("scale on fossil ggtree", gg)
skip_if(R.Version()$os != "mingw32") # only test this on Windows
gg <- ggtree(ceratopsianTreeRaia,
position = position_nudge(x = -ceratopsianTreeRaia$root.time)) +
coord_geo_polar(dat = list("stages", "periods"),
lab = list(FALSE, TRUE), abbrv = TRUE) +
scale_x_continuous(expand = expansion(add = c(20, 30)))
expect_doppelganger_deeptime("scale on fossil ggtree with labels", gg)
})
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