Start with basic suite of functionality tests. [skip ci]

R/PAVER_export.R

@@ -6,7 +6,7 @@
 #' of each GO term for that group.
 #'
 #' @param PAVER_result A PAVER result object generated by the \code{\link{generate_themes}} function.
-#' @return A wide format data frame with GO Term IDs, Definitions, gererated themes, and columns
+#' @return A wide format data frame with GO Term IDs, Definitions, generated themes, and columns
 #' for each of the groups in the PAVER result, with values representing the original input value
 #' of each GO term for that group.
 #'

tests/testthat/test-PAVER_combined_plot.R

@@ -0,0 +1,23 @@
+library(testthat)
+library(ggplot2)
+library(ggpubr)
+
+test_that("PAVER_combined_plot works correctly", {
+
+  #Use vignette example data
+  input = gsea_example
+
+  embeddings = readRDS(url("https://github.com/willgryan/PAVER_embeddings/raw/main/2023-03-06/embeddings_2023-03-06.RDS"))
+
+  ontology_index = readRDS(url("https://github.com/willgryan/PAVER_embeddings/raw/main/2023-03-06/ontology_2023-03-06.RDS"))
+
+  PAVER_result <- prepare_data(input, embeddings, ontology_index)
+
+  PAVER_result <- generate_themes(PAVER_result, minClusterSize = 40)
+
+  # Run the function and catch the result
+  p <- PAVER_combined_plot(PAVER_result)
+
+  # Verify the function runs and produces a ggplot object
+  expect_s3_class(p, "gg")
+})

tests/testthat/test-PAVER_export.R

@@ -0,0 +1,27 @@
+library(testthat)
+library(dplyr)
+library(tidyr)
+library(tibble)
+
+test_that("PAVER_export works correctly", {
+
+  #Use vignette example data
+  input = gsea_example
+
+  embeddings = readRDS(url("https://github.com/willgryan/PAVER_embeddings/raw/main/2023-03-06/embeddings_2023-03-06.RDS"))
+
+  ontology_index = readRDS(url("https://github.com/willgryan/PAVER_embeddings/raw/main/2023-03-06/ontology_2023-03-06.RDS"))
+
+  PAVER_result <- prepare_data(input, embeddings, ontology_index)
+
+  PAVER_result <- generate_themes(PAVER_result, minClusterSize = 40)
+
+  # Test PAVER_export function
+  export_result <- PAVER_export(PAVER_result)
+
+  # Verify the structure and content of the output
+  expect_s3_class(export_result, "tbl_df")
+  expect_gte(ncol(export_result), 3)
+  expect_equal(names(export_result)[1:3], c("GOID", "Cluster", "Term"))
+
+})

tests/testthat/test-PAVER_hunter_plot.R

@@ -0,0 +1,23 @@
+library(testthat)
+library(ggplot2)
+library(ggpubr)
+
+test_that("PAVER_hunter_plot works correctly", {
+
+  #Use vignette example data
+  input = gsea_example
+
+  embeddings = readRDS(url("https://github.com/willgryan/PAVER_embeddings/raw/main/2023-03-06/embeddings_2023-03-06.RDS"))
+
+  ontology_index = readRDS(url("https://github.com/willgryan/PAVER_embeddings/raw/main/2023-03-06/ontology_2023-03-06.RDS"))
+
+  PAVER_result <- prepare_data(input, embeddings, ontology_index)
+
+  PAVER_result <- generate_themes(PAVER_result, minClusterSize = 40)
+
+  # Run the function and catch the result
+  p <- PAVER_hunter_plot(PAVER_result)
+
+  # Verify the function runs and produces a ggplot object
+  expect_s4_class(p, "HeatmapList")
+})

tests/testthat/test-PAVER_interpretation_plot.R

@@ -0,0 +1,23 @@
+library(testthat)
+library(ggplot2)
+library(ggpubr)
+
+test_that("PAVER_interpretation_plot works correctly", {
+
+  #Use vignette example data
+  input = gsea_example
+
+  embeddings = readRDS(url("https://github.com/willgryan/PAVER_embeddings/raw/main/2023-03-06/embeddings_2023-03-06.RDS"))
+
+  ontology_index = readRDS(url("https://github.com/willgryan/PAVER_embeddings/raw/main/2023-03-06/ontology_2023-03-06.RDS"))
+
+  PAVER_result <- prepare_data(input, embeddings, ontology_index)
+
+  PAVER_result <- generate_themes(PAVER_result, minClusterSize = 40)
+
+  # Run the function and catch the result
+  p <- PAVER_interpretation_plot(PAVER_result)
+
+  # Verify the function runs and produces a ggplot object
+  expect_s3_class(p, "gg")
+})

tests/testthat/test-PAVER_regulation_plot.R

@@ -0,0 +1,23 @@
+library(testthat)
+library(ggplot2)
+library(ggpubr)
+
+test_that("PAVER_regulation_plot works correctly", {
+
+  #Use vignette example data
+  input = gsea_example
+
+  embeddings = readRDS(url("https://github.com/willgryan/PAVER_embeddings/raw/main/2023-03-06/embeddings_2023-03-06.RDS"))
+
+  ontology_index = readRDS(url("https://github.com/willgryan/PAVER_embeddings/raw/main/2023-03-06/ontology_2023-03-06.RDS"))
+
+  PAVER_result <- prepare_data(input, embeddings, ontology_index)
+
+  PAVER_result <- generate_themes(PAVER_result, minClusterSize = 40)
+
+  # Run the function and catch the result
+  p <- PAVER_regulation_plot(PAVER_result)
+
+  # Verify the function runs and produces a ggplot object
+  expect_s3_class(p, "gg")
+})

tests/testthat/test-PAVER_theme_plot.R

@@ -0,0 +1,23 @@
+library(testthat)
+library(ggplot2)
+library(ggpubr)
+
+test_that("PAVER_theme_plot works correctly", {
+
+  #Use vignette example data
+  input = gsea_example
+
+  embeddings = readRDS(url("https://github.com/willgryan/PAVER_embeddings/raw/main/2023-03-06/embeddings_2023-03-06.RDS"))
+
+  ontology_index = readRDS(url("https://github.com/willgryan/PAVER_embeddings/raw/main/2023-03-06/ontology_2023-03-06.RDS"))
+
+  PAVER_result <- prepare_data(input, embeddings, ontology_index)
+
+  PAVER_result <- generate_themes(PAVER_result, minClusterSize = 40)
+
+  # Run the function and catch the result
+  p <- PAVER_theme_plot(PAVER_result)
+
+  # Verify the function runs and produces a ggplot object
+  expect_s3_class(p, "gg")
+})

tests/testthat/test-generate_themes.R

@@ -0,0 +1,33 @@
+library(testthat)
+library(dplyr)
+library(tidyr)
+library(tibble)
+library(magrittr)
+library(umap)
+library(dynamicTreeCut)
+library(randomcoloR)
+
+test_that("generate_themes works correctly", {
+
+  #Use vignette example data
+  input = gsea_example
+
+  embeddings = readRDS(url("https://github.com/willgryan/PAVER_embeddings/raw/main/2023-03-06/embeddings_2023-03-06.RDS"))
+
+  ontology_index = readRDS(url("https://github.com/willgryan/PAVER_embeddings/raw/main/2023-03-06/ontology_2023-03-06.RDS"))
+
+  PAVER_result <- prepare_data(input, embeddings, ontology_index)
+
+  # Test generate_themes function
+  result <- generate_themes(PAVER_result, minClusterSize = 40)
+
+  # Verify output structure
+  expect_type(result, "list")
+  expect_named(result, c("prepared_data", "embedding_mat", "umap", "goterms_df", "clustering", "avg_cluster_embeddings", "mds", "colors"))
+  expect_s3_class(result$clustering, "tbl_df")
+  expect_s3_class(result$avg_cluster_embeddings, "tbl_df")
+  expect_s3_class(result$mds, "smacof")
+  expect_type(result$colors, "character")
+
+})
+

tests/testthat/test-prepare_data.R

@@ -0,0 +1,29 @@
+library(testthat)
+library(dplyr)
+library(tidyr)
+library(tibble)
+library(magrittr)
+library(umap)
+
+test_that("prepare_data works correctly", {
+
+  #Use vignette example data
+  input = gsea_example
+
+  embeddings = readRDS(url("https://github.com/willgryan/PAVER_embeddings/raw/main/2023-03-06/embeddings_2023-03-06.RDS"))
+
+  ontology_index = readRDS(url("https://github.com/willgryan/PAVER_embeddings/raw/main/2023-03-06/ontology_2023-03-06.RDS"))
+
+  # Test function
+  result <- prepare_data(input, embeddings, ontology_index)
+
+  # Verify output structure
+  expect_type(result, "list")
+  expect_named(result, c("prepared_data", "embedding_mat", "umap", "goterms_df"))
+  expect_s3_class(result$prepared_data, "data.frame")
+  expect_s3_class(result$embedding_mat, "tbl_df")
+  expect_s3_class(result$umap, "umap")
+  expect_s3_class(result$goterms_df, "tbl_df")
+
+})
+