tests/testthat/test-ggdend.R

In talgalili/dendextend: Extending 'dendrogram' Functionality in R

# library(testthat)


# fixing how the tests are printed
# cat("\n")

context("ggdend")


test_that("as.ggdend.dendrogram works", {


  # get_nodes_attr(d1, "nodePar", simplify = FALSE)
  # plot(d1)

  dend <- 1:3 %>%
    dist() %>%
    hclust() %>%
    as.dendrogram() %>%
    set("branches_k_color", k = 2) %>%
    set("branches_lwd", c(1.5, 1, 1.5)) %>%
    set("branches_lty", c(1, 1, 3, 1, 1, 2)) %>%
    set("labels_colors") %>%
    set("labels_cex", c(.9, 1.2)) %>%
    set("nodes_pch", 19) %>%
    set("nodes_col", c("orange", "black", "NA"))

  gg1 <- as.ggdend(dend)
  # ggplot(gg1)
  # dput(gg1)
  should_be <- structure(list(
    segments = structure(list(x = c(
      1.75, 1, 1.75,
      2.5, 2.5, 2, 2.5, 3
    ), y = c(2, 2, 2, 2, 1, 1, 1, 1), xend = c(
      1,
      1, 2.5, 2.5, 2, 2, 3, 3
    ), yend = c(2, 0, 2, 1, 1, 0, 1, 0), col = c(
      "#CC476B",
      "#CC476B", "#009681", "#009681", "#009681", "#009681", "#009681",
      "#009681"
    ), lwd = c(1, 1, 1.5, 1.5, 1.5, 1.5, 1, 1), lty = c(
      1,
      1, 3, 3, 1, 1, 1, 1
    )), .Names = c(
      "x", "y", "xend", "yend", "col",
      "lwd", "lty"
    ), row.names = c(NA, 8L), class = "data.frame"),
    labels = structure(list(x = c(1, 2, 3), y = c(0, 0, 0), label = structure(1:3, .Label = c(
      "3",
      "1", "2"
    ), class = "factor"), col = c(
      "#CC476B", "#228B00",
      "#0082CE"
    ), cex = c(0.9, 1.2, 0.9)), .Names = c(
      "x", "y",
      "label", "col", "cex"
    ), row.names = c(NA, 3L), class = "data.frame"),
    nodes = structure(list(x = c(1.75, 1, 2.5, 2, 3), y = c(
      2,
      0, 1, 0, 0
    ), pch = c(19, 19, 19, 19, 19), cex = c(
      NA, NA,
      NA, NA, NA
    ), col = c("orange", "black", "NA", "orange", "black"), members = c(3L, 1L, 2L, 1L, 1L), midpoint = c(
      0.75, NA,
      0.5, NA, NA
    ), height = c(2, 0, 1, 0, 0), leaf = c(
      NA, TRUE,
      NA, TRUE, TRUE
    )), .Names = c(
      "x", "y", "pch", "cex", "col",
      "members", "midpoint", "height", "leaf"
    ), row.names = c(
      NA,
      -5L
    ), class = "data.frame")
  ), .Names = c(
    "segments", "labels",
    "nodes"
  ), class = "ggdend")
  expect_identical(gg1, should_be)



  dend <- 1:3 %>%
    dist() %>%
    hclust() %>%
    as.dendrogram()
  gg2 <- as.ggdend(dend)
  #    dput(gg2)
  should_be <- structure(list(segments = structure(list(x = c(
    1.75, 1, 1.75,
    2.5, 2.5, 2, 2.5, 3
  ), y = c(2, 2, 2, 2, 1, 1, 1, 1), xend = c(
    1,
    1, 2.5, 2.5, 2, 2, 3, 3
  ), yend = c(2, 0, 2, 1, 1, 0, 1, 0), col = c(
    NA,
    NA, NA, NA, NA, NA, NA, NA
  ), lwd = c(
    NA, NA, NA, NA, NA, NA,
    NA, NA
  ), lty = c(NA, NA, NA, NA, NA, NA, NA, NA)), .Names = c(
    "x",
    "y", "xend", "yend", "col", "lwd", "lty"
  ), row.names = c(
    NA,
    8L
  ), class = "data.frame"), labels = structure(list(x = c(
    1,
    2, 3
  ), y = c(0, 0, 0), label = structure(1:3, .Label = c(
    "3",
    "1", "2"
  ), class = "factor"), col = c(NA, NA, NA), cex = c(
    NA,
    NA, NA
  )), .Names = c("x", "y", "label", "col", "cex"), row.names = c(
    NA,
    3L
  ), class = "data.frame"), nodes = structure(list(
    x = c(
      1.75,
      1, 2.5, 2, 3
    ), y = c(2, 0, 1, 0, 0), pch = c(
      NA, NA, NA, NA,
      NA
    ), cex = c(NA, NA, NA, NA, NA), col = c(NA, NA, NA, NA, NA),
    members = c(3L, 1L, 2L, 1L, 1L), midpoint = c(
      0.75, NA, 0.5,
      NA, NA
    ), height = c(2, 0, 1, 0, 0), leaf = c(
      NA, TRUE, NA,
      TRUE, TRUE
    )
  ), .Names = c(
    "x", "y", "pch", "cex", "col", "members",
    "midpoint", "height", "leaf"
  ), row.names = c(NA, -5L), class = "data.frame")), .Names = c(
    "segments",
    "labels", "nodes"
  ), class = "ggdend")
  ###
  expect_identical(gg2, should_be)
})

test_that("ggplot doesn't have warnings for dendrograms", {
  library(ggplot2)
  library(dendextend)
  g <- ggplot(as.dendrogram(hclust(dist(mtcars))))
  expect_warning(ggplot_build(g), NA)
})




# library(testthat)
# library(dendextend)

# Testing ggdend function
test_that("ggdend provides usage message", {
   expect_output(ggdend(), "Use either as.ggdend or ggplot (or both). ", fixed = TRUE)
})

# Testing allNA function
test_that("allNA correctly identifies all NA values", {
   allNA <- dendextend:::allNA
   expect_true(dendextend:::allNA(c(NA, NA, NA)))
   expect_false(allNA(c(1, NA, 3)))
})

# Testing as.ggdend.dendrogram function
test_that("as.ggdend.dendrogram stops with non-dendrogram input", {
   as.ggdend.dendrogram <- dendextend:::as.ggdend.dendrogram
   expect_error(as.ggdend.dendrogram(list()), "dend is not a dendrogram")
})

test_that("as.ggdend.dendrogram stops with empty dendrogram", {
   as.ggdend.dendrogram <- dendextend:::as.ggdend.dendrogram
   empty_dend <- list()
   class(empty_dend) <- "dendrogram"
   expect_error(as.ggdend.dendrogram(empty_dend), "argument is of length zero")
})

test_that("as.ggdend.dendrogram stops with edge.root argument", {
   as.ggdend.dendrogram <- dendextend:::as.ggdend.dendrogram
   dend <- as.dendrogram(hclust(dist(1:5)))
   expect_error(as.ggdend.dendrogram(dend, edge.root = TRUE), "edge.root is not supported")
})

test_that("as.ggdend.dendrogram returns ggdend class with valid input", {
   as.ggdend.dendrogram <- dendextend:::as.ggdend.dendrogram
   dend <- as.dendrogram(hclust(dist(1:5)))
   result <- as.ggdend.dendrogram(dend)
   expect_true("ggdend" %in% class(result))
})

# Testing prepare.ggdend function
test_that("prepare.ggdend handles segment linetype and color", {
   dend <- as.dendrogram(hclust(dist(1:5)))
   ggdend_data <- as.ggdend(dend)
   prepared_data <- prepare.ggdend(ggdend_data)
   
   # Check for linetype and color corrections
   expect_true(all(!is.na(prepared_data$segments$lty)))
   expect_true(all(!is.na(prepared_data$segments$col)))
})

# Testing ggplot.ggdend function
test_that("ggplot.ggdend creates a ggplot object", {
   ggplot.ggdend <- dendextend:::ggplot.ggdend
   dend <- as.dendrogram(hclust(dist(1:5)))
   ggdend_data <- as.ggdend(dend)
   plot <- ggplot.ggdend(ggdend_data)
   expect_true(inherits(plot, "ggplot"))
})

# Testing ggplot.dendrogram function
test_that("ggplot.dendrogram converts dendrogram to ggplot", {
   ggplot.dendrogram <- dendextend:::ggplot.dendrogram
   dend <- as.dendrogram(hclust(dist(1:5)))
   plot <- ggplot.dendrogram(dend)
   expect_true(inherits(plot, "ggplot"))
})


test_that("print.ggdend prints a ggplot", {
   dend <- as.dendrogram(hclust(dist(1:5)))
   ggdend_data <- as.ggdend(dend)
   pdf(file = NULL)  # Open a null device
   expect_silent(print(ggdend_data))
   dev.off()  # Close the null device
   expect_true(inherits(ggdend_data, "ggdend"))  # check if it's a ggdend object
   expect_true(inherits(ggplot2::ggplot(ggdend_data), "ggplot"))  # check if it can be used to create a ggplot object
})