tests/testthat/test-geom_signific_basic.R

In const-ae/ggsignif: Significance Brackets for 'ggplot2'

library(ggplot2)

test_that("the plotting works", {
  print(
    ggplot(mpg, aes(x = manufacturer, y = displ)) +
      geom_boxplot() +
      stat_signif(
        comparisons = list(c("audi", "ford"), c("hyundai", "nissan")),
        map_signif_level = TRUE,
        test = "wilcox.test", test.args = list(alternative = "two.sided"),
        margin_top = 0.02, step_increase = 0, tip_length = 0.01
      ) +
      theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
      facet_wrap(~ as.factor(year), scale = "free")
  )
  expect_equal(1, 1)
})

test_that("geom works as well as stat works", {
  print(
    ggplot(mpg, aes(x = manufacturer, y = displ)) +
      geom_boxplot() +
      geom_signif(
        comparisons = list(c("audi", "ford"), c("hyundai", "nissan")),
        annotations = c("Interesting", "Too far apart"),
        # map_signif_level=TRUE,
        test = "wilcox.test", test.args = list(alternative = "two.sided"),
        margin_top = 0.02, step_increase = 0, tip_length = 0.01
      ) +
      theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
      facet_wrap(~ as.factor(year), scale = "free")
  )
  expect_equal(1, 1)
})


test_that("non-sense gives warning", {
  expect_warning(print(
    ggplot(mpg, aes(y = hwy, x = displ, group = manufacturer)) +
      geom_point() +
      stat_signif(comparisons = list(c("audi", "ford"), c("hyundai", "nissan")))
  ))
})


test_that("geom_signif with identity works", {
  dat <- data.frame(
    Group = c("S1", "S1", "S2", "S2"),
    Sub = c("A", "B", "A", "B"),
    Value = c(3, 5, 7, 8)
  )

  ## Define base plot
  print(
    ggplot(dat, aes(Group, Value)) +
      geom_bar(aes(fill = Sub),
        stat = "identity",
        position = "dodge",
        width = .5
      ) +
      geom_signif(
        stat = "identity",
        data = data.frame(
          m = c(0.875, 1.875),
          xend = c(1.125, 2.125),
          n = c(5.8, 8.5),
          annotation = c("***", "NS")
        ),
        aes(
          x = m,
          xend = xend,
          y = n,
          yend = n,
          annotation = annotation
        )
      ) +
      geom_signif(
        comparisons = list(c("S1", "S2")),
        annotations = "***",
        y_position = 9.3,
        tip_length = 0
      ) +
      scale_fill_manual(values = c("grey80", "grey20"))
  )
  expect_equal(1, 1)
})



test_that("you can change the linetype", {
  print(
    ggplot(iris, aes(x = Species, y = Sepal.Length)) +
      geom_boxplot() +
      geom_signif(
        comparisons = list(c("versicolor", "virginica")),
        map_signif_level = TRUE,
        linetype = 3,
        alpha = 1,
        color = "blue",
        size = 1,
        textsize = 8
      ) +
      ylim(c(NA, 8.5))
  )
  expect_equal(1, 1)
})


test_that("identical annotations are plotted separetly", {
  dat <- data.frame(
    Group = c("S1", "S1", "S2", "S2"),
    Sub = c("A", "B", "A", "B"),
    Value = c(3, 5, 7, 8)
  )

  print(
    ggplot(dat, aes(Group, Value)) +
      geom_bar(aes(fill = Sub), stat = "identity", position = "dodge", width = .5) +
      geom_signif(
        comparisons = list(c("S1", "S2")), annotations = "***",
        y_position = 9.3, tip_length = 0, vjust = 0.4
      ) +
      geom_signif(
        stat = "identity",
        data = data.frame(
          x = c(0.875, 1.875), xend = c(1.125, 2.125),
          y = c(5.8, 8.5), annotation = c("**", "**")
        ),
        aes(
          x = x,
          xend = xend,
          y = y,
          yend = y,
          annotation = annotation,
          group = c(1, 2)
        )
      ) +
      scale_fill_manual(values = c("grey80", "grey20"))
  )
  expect_equal(1, 1)
})

test_that("multiple comparisons can be made to the same element", {
  set.seed(1)
  print(
    ggplot(
      data.frame(y = runif(100), x = sample(c("A", "B", "C", "D"), size = 100, replace = TRUE)),
      aes(x = x, y = y)
    ) +
      geom_boxplot() +
      geom_signif(
        comparisons = list(c(1, 2), c(2, 3), c(1, 3), c(1, 4), c(2, 4), c(1, 2)),
        step_increase = .1
      )
  )
  expect_equal(1, 1)
})


test_that("plots with xmin, xmax work", {
  library(datasets)

  data(airquality)
  airquality$Month <- factor(airquality$Month,
    labels = c("May", "Jun", "Jul", "Aug", "Sep")
  )
  airquality_trimmed <- airquality[which(airquality$Month == "Jul" |
    airquality$Month == "Aug" |
    airquality$Month == "Sep"), ]
  airquality_trimmed$Temp.f <- factor(ifelse(airquality_trimmed$Temp > mean(airquality_trimmed$Temp), 1, 0),
    labels = c("Low temp", "High temp")
  )

  print(ggplot(airquality_trimmed, aes(x = Month, y = Ozone, fill = Temp.f)) +
    geom_boxplot(alpha = 0.7, width = 0.4) +
    geom_signif(
      y_position = 150, xmin = c(0.9, 1.9), xmax = c(1.1, 2.1),
      annotations = c("***", "NS")
    ) +
    scale_y_continuous(
      name = "Mean ozone in\nparts per billion",
      breaks = seq(0, 175, 25),
      limits = c(0, 175)
    ) +
    scale_x_discrete(name = "Month") +
    ggtitle("Boxplot of mean ozone by month") +
    theme_bw() +
    theme(
      plot.title = element_text(size = 14, face = "bold"),
      text = element_text(size = 12),
      axis.title = element_text(face = "bold"),
      axis.text.x = element_text(size = 11),
      legend.position = "bottom"
    ) +
    scale_fill_brewer(palette = "Accent") +
    labs(fill = "Temperature"))
  expect_equal(1, 1)
})


test_that("manually annotated plots work", {
  ggplot(
    data = diamonds,
    aes(
      x = cut,
      y = price
    )
  ) +
    geom_boxplot() +
    geom_signif(
      data = data.frame(
        color = c("E", "E", "G"),
        annotations = c("123", "abc", "xyz"),
        xmin = c(1, 4, 2),
        xmax = c(2, 3, 3)
      ),
      aes(annotations = annotations, xmin = xmin, xmax = xmax),
      manual = TRUE,
      y_position = 20000
    ) +
    facet_wrap(~color) +
    ylim(NA, 22000)
  expect_equal(1, 1)
})

test_that("test method which return text work", {
  magnitude_test <- function(x, y, ...) {
    change <- mean(y) / mean(x)
    p <- t.test(x, y)$p.value
    stars <- if (p < 0.001) {
      "***"
    } else if (p < 0.01) {
      "**"
    } else if (p < 0.05) {
      "*"
    } else {
      ""
    }
    list(p.value = paste0(signif(change, digits = 2), stars))
  }

  ggplot(mpg, aes(x = manufacturer, y = displ)) +
    geom_boxplot() +
    stat_signif(
      comparisons = list(c("audi", "ford"), c("hyundai", "nissan")),
      test = magnitude_test,
      margin_top = 0.02, step_increase = 0, tip_length = 0.01
    ) +
    theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
    facet_wrap(~ as.factor(year), scale = "free")
  expect_equal(1, 1)
})