tests/testthat/test-kmeans.R

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

context("Test Kmeans and plotting functions")
library(musicatk)

test_that(desc = "Test plotting function for selecting k", {
  data(res_annot)
  p <- k_select(res_annot, method = "wss", n = 6)
  expect_true(ggplot2::is.ggplot(p))
  p <- k_select(res_annot, method = "silhouette", n = 6)
  expect_true(ggplot2::is.ggplot(p))
  p <- k_select(res_annot, method = "gap_stat", n =6)
  expect_true(ggplot2::is.ggplot(p))
})

test_that(desc = "Test kmeans visualization function", {
  data(res_annot)
  expect_error(cluster_exposure(result = res_annot, nclust = 2, method = "hkmeans", dis.method = "cosine"), "For hkmeans clustering")
  expect_error(cluster_exposure(result = res_annot, nclust = 2, method = "clara", dis.method = "cosine"), "For clara clustering")
  clust_out <- cluster_exposure(result = res_annot, nclust = 2)
  expect_equal(nrow(clust_out), 7)
  expect_error(plot_cluster(result = res_annot, clusters = clust_out, group = "signature"), "UMAP not found")
  expect_error(plot_cluster(result = res_annot, clusters = clust_out, group = "annotation"), "UMAP not found")
  expect_error(plot_cluster(result = res_annot, clusters = clust_out, group = "none"), "UMAP not found")
  create_umap(res_annot)
  test_res <- res_annot
  test_res@musica@sample_annotations <- samp_annot(res_annot)[,-2]
  expect_error(plot_cluster(result = test_res, clusters = clust_out, group = "annotation"), "Sample annotation not found")
  expect_error(plot_cluster(result = res_annot, clusters = clust_out, group = "annotation", annotation = "cancer"), "invalid annotation column name")
  p <- plot_cluster(result = res_annot, clusters = clust_out, group = "signature", plotly = FALSE)
  expect_true(ggplot2::is.ggplot(p))
  p <- plot_cluster(result = res_annot, clusters = clust_out, group = "annotation", annotation = "Tumor_Subtypes", plotly = FALSE)
  expect_true(ggplot2::is.ggplot(p))
  p <- plot_cluster(result = res_annot, clusters = clust_out, group = "none", plotly = FALSE)
  expect_true(ggplot2::is.ggplot(p))
})