more tests!

Author: rmflight

NEWS.md

@@ -1,3 +1,7 @@
+# categoryCompare2 0.200.9
+
+- added more tests to up the test coverage, and hopefully a test coverage badge.
+
 # categoryCompare2 0.200.8
 
 - fixes a long standing non-standard evaluation bug where if you tried to use an argument in a filtering operation, it would fail if it was within another function, or run in another process (#29).

R/graph_visualization.R

@@ -221,7 +221,7 @@ assign_colors <- function(in_assign, type = "experiment") {
 #' @return list of png files that are pie graphs
 #' @importFrom colorspace desaturate
 generate_piecharts <- function(grp_matrix, use_color) {
-  check_package_installed("Cairo")
+  check_package_installed("ragg")
   n_grp <- nrow(grp_matrix)
   n_color <- length(use_color)
 
@@ -250,12 +250,12 @@ generate_piecharts <- function(grp_matrix, use_color) {
     )
 
     out_file <- tempfile(i_grp, fileext = ".png")
-    Cairo::Cairo(
+    ragg::agg_png(
+      filename = out_file,
+      units = "px",
       width = 640,
       height = 640,
-      file = out_file,
-      type = "png",
-      bg = "transparent"
+      background = "transparent"
     )
     par(mai = c(0, 0, 0, 0))
     pie(pie_area, col = tmp_color, clockwise = TRUE)
@@ -503,7 +503,7 @@ setMethod(
 #' @param img should a base64 encoded data uri be returned for embedding?
 #' @param width how wide should the image be if saving to an image
 #' @param height how high should it be
-#' @param pointsize the pointsize parameter for Cairo, determines textsize in the image
+#' @param pointsize the pointsize parameter for ragg, determines textsize in the image
 #' @param ... any other parameter to \code{pie}
 #'
 #' @return NULL
@@ -533,11 +533,11 @@ generate_legend <- function(
       par(mai = c(0, 0, 0, 0), ps = pointsize)
       pie(pie_area, labels = use_labels, col = use_color, clockwise = TRUE, ...)
     } else {
-      check_package_installed("Cairo")
+      check_package_installed("ragg")
       out_file <- tempfile(pattern = "legendfile", fileext = ".png")
-      Cairo::CairoPNG(
-        file = out_file,
-        bg = "white",
+      ragg::agg_png(
+        filename = out_file,
+        background = "white",
         width = width,
         height = height,
         pointsize = pointsize

R/managing_annotations.R

@@ -243,7 +243,7 @@ json_2_annotation <- function(json_file) {
 #'
 #' @importFrom jsonlite fromJSON toJSON
 #' @export
-#' @return the json object, invisibly
+#' @return the json file
 #'
 json_annotation_reversal <- function(
   json_file,
@@ -294,5 +294,5 @@ json_annotation_reversal <- function(
   )
 
   out_json <- annotation_2_json(out_annotation, out_file)
-  out_json
+  invisible(out_file)
 }

README.md

@@ -1,3 +1,6 @@
+[![categoryCompare2 status badge](https://moseleybioinformaticslab.r-universe.dev/badges/categoryCompare2)](https://moseleybioinformaticslab.r-universe.dev/categoryCompare2)
+[![covr2gh coverage](https://raw.githubusercontent.com/MoseleyBioinformaticsLab/categoryCompare2/refs/heads/covr2gh-storage/badges/main/coverage_badge.svg)](https://github.com/MoseleyBioinformaticsLab/categoryCompare2/actions/workflows/covr2gh.yaml)
+
 # categoryCompare2
 
 A Bioconductor package for meta analysis of high-throughput datasets using 

tests/testthat/test-db-annotations.R

@@ -0,0 +1,35 @@
+test_that("annotations from db work", {
+  entrez_db = get_db_annotation()
+
+  expect_equal(
+    entrez_db@annotation_features[1],
+    list(`GO:0000009` = c("55650", "79087", "85365"))
+  )
+
+  ensembl_db = get_db_annotation(feature_type = "ENSEMBL")
+  expect_equal(
+    ensembl_db@annotation_features[1],
+    list(
+      `GO:0000009` = c("ENSG00000060642", "ENSG00000182858", "ENSG00000119523")
+    )
+  )
+
+  entrez_cc = get_db_annotation(annotation_type = "CC")
+  cc_desc = head(entrez_cc@description)
+  expect_all_true(grepl("complex", cc_desc))
+
+  entrez_pmid = get_db_annotation(annotation_type = "PMID")
+  expect_equal(
+    entrez_pmid@annotation_features["100103"],
+    list(
+      `100103` = c(
+        "100008587",
+        "106632260",
+        "106632261",
+        "106632262",
+        "106632263"
+      )
+    )
+  )
+  expect_equal(entrez_pmid@annotation_type, "PMID")
+})

tests/testthat/test-gocats.R

@@ -101,3 +101,28 @@ test_that("json exporting and importing works properly", {
     expect_equal(without_namespace2, in_annotation)
   })
 })
+
+test_that("json reversal works", {
+  withr::with_file("reversed.json", {
+    out_res = json_annotation_reversal(
+      ancestors_file,
+      out_file = "reversed.json"
+    )
+    tmp_json = jsonlite::fromJSON("reversed.json", simplifyVector = FALSE)
+    expect_equal(
+      names(tmp_json),
+      c("annotation_features", "counts", "annotation_type", "feature_type")
+    )
+    expect_equal(
+      head(names(tmp_json$annotation_features)),
+      c(
+        "GO:0000002",
+        "GO:0000003",
+        "GO:0000009",
+        "GO:0000010",
+        "GO:0000012",
+        "GO:0000014"
+      )
+    )
+  })
+})

tests/testthat/test-graph_creation.R

@@ -37,7 +37,7 @@ test_that("various graph properties are correct", {
   expect_equal(combined_coefficient(group3, group4), 8 / 15)
   expect_equal(combined_coefficient(group1, character()), NaN)
 
-  # generating simple graphs
+  # generating simple graphs ---------
   group5 <- letters[10:12]
   group6 <- letters[11:12]
 
@@ -68,7 +68,7 @@ test_that("various graph properties are correct", {
 })
 
 
-test_that('extraction of significant to graph is correct', {
+test_that('extraction of significant to graph works', {
   set.seed(1234)
   random_genes = sample(enrichment_data$universe, 100)
   non_enriched = hypergeometric_feature_enrichment(
@@ -80,14 +80,114 @@ test_that('extraction of significant to graph is correct', {
     ),
     p_adjust = "BH"
   )
+
+  # checking for warnings -------------
   non_list = combine_enrichments(c1 = non_enriched)
   non_sig = get_significant_annotations(non_list, padjust <= 0.01)
   expect_warning(
     generate_annotation_graph(non_sig, low_cut = 2, hi_cut = 1000),
     regexp = "Nothing significant"
   )
 
+  # and that we get a 27 member network -------------
   non_sig2 = get_significant_annotations(non_list, p <= 0.01)
   sig2_graph = generate_annotation_graph(non_sig2, low_cut = 2, hi_cut = 1000)
   expect_equal(graph::numNodes(sig2_graph), 27)
+
+  # checking that tooltips get added ------------
+  sig2_graph_tooltips = add_tooltip(
+    sig2_graph,
+    description = non_sig2@annotation@description[graph::nodes(sig2_graph)]
+  )
+  expect_equal(
+    graph::nodeData(sig2_graph_tooltips, "GO:0000086", "tooltip"),
+    list(
+      `GO:0000086` = "GO:0000086\nG2/M transition of mitotic cell cycle\nG2/M transition of mitotic cell cycle"
+    )
+  )
+
+  # can generate communities ---------------
+  sig2_comms = assign_communities(sig2_graph_tooltips)
+  sig2_labels = label_communities(sig2_comms, non_sig2@annotation)
+  expect_equal(length(sig2_comms), 7)
+  expect_equal(length(sig2_labels), 5)
+  expect_equal(
+    sig2_labels[[1]],
+    list(
+      rep = "GO:1905114",
+      label = "cell surface receptor signaling pathway involved in cell-cell signaling",
+      members = c(
+        "GO:0002524",
+        "GO:0021545",
+        "GO:0038166",
+        "GO:0042249",
+        "GO:1905114"
+      )
+    )
+  )
+
+  bare_table = table_from_graph(sig2_graph_tooltips)
+  expect_equal(nrow(bare_table), 27)
+
+  tmp_combinations = annotation_combinations(sig2_graph_tooltips)
+  tmp_combinations = assign_colors(tmp_combinations)
+  comm_table = table_from_graph(
+    sig2_graph_tooltips,
+    in_assign = tmp_combinations
+  )
+  expect_equal(nrow(comm_table), nrow(bare_table))
+
+  group_table = table_from_graph(
+    sig2_graph_tooltips,
+    tmp_combinations,
+    sig2_labels
+  )
+  expect_gt(nrow(group_table), nrow(bare_table))
+  expect_equal(group_table$c1.p[1], NA_real_)
+})
+
+test_that("check packages installed works", {
+  expect_null(check_package_installed("stats"))
+  withr::with_temp_libpaths(
+    {
+      expect_error(check_package_installed("Cairo"), "is not installed")
+    },
+    action = "replace"
+  )
+})
+
+test_that("colors come out correctly", {
+  expect_equal(
+    generate_colors(4),
+    c("#FF7A9E", "#AAB500", "#00CEB7", "#AC9AFF")
+  )
+  expect_equal(
+    generate_colors(5),
+    c("#FF7A9E", "#00CA66", "#DA88FF", "#CAAA00", "#00C6F2")
+  )
+})
+
+test_that("modifying graphs works", {
+  group1 <- letters[1:6]
+  group2 <- group1
+  group3 <- letters[1:3]
+  group4 <- letters[c(1, 2, 8, 10)]
+
+  group5 <- letters[10:12]
+  group6 <- letters[11:12]
+
+  feature_list <- list(
+    g1 = group1,
+    g2 = group2,
+    g3 = group3,
+    g4 = group4,
+    g5 = group5,
+    g6 = group6
+  )
+
+  test_combined = generate_annotation_similarity_graph(feature_list)
+  # removing edges is correct ------------
+  # remove edges < 0.75, results in 4 edges left
+  remove_07 = remove_edges(test_combined, 0.75)
+  expect_equal(length(graph::edgeData(remove_07, attr = "weight")), 4)
 })

tests/testthat/test-significant_results.R

@@ -134,6 +134,24 @@ test_that("get correct sig annotations from combined_enrichment", {
     expected_sig_combined,
     get_significant_annotations(test_combined, pvalues < 0.05)
   )
+
+  expected_sig = new(
+    "node_assign",
+    groups = structure(
+      c(TRUE, TRUE, FALSE, TRUE, FALSE, TRUE),
+      dim = 3:2,
+      dimnames = list(c("G1", "G2", "G3"), c("en1", "en2"))
+    ),
+    assignments = c(a1 = "G1", a2 = "G3", a3 = "G2", a4 = "G3"),
+    description = c(a1 = "en1,en2", a2 = "en2", a3 = "en1", a4 = "en2"),
+    colors = character(0),
+    color_type = character(0),
+    pie_locs = NULL
+  )
+  expect_equal(
+    expected_sig,
+    annotation_combinations(expected_significant_annotations)
+  )
 })
 
 
@@ -208,4 +226,26 @@ test_that("get correct sig annotations from combined_enrichment with single case
     expected_single_combined,
     get_significant_annotations(single_combined, pvalues < 0.05)
   )
+
+  # check annotation_combinations --------
+  exp_sig = new(
+    "node_assign",
+    groups = structure(
+      c(TRUE, FALSE),
+      dim = 2:1,
+      dimnames = list(
+        c("G1", "G2"),
+        "en1"
+      )
+    ),
+    assignments = c(a1 = "G1", a2 = "G2", a3 = "G1"),
+    description = c(a1 = "en1", a2 = "", a3 = "en1"),
+    colors = character(0),
+    color_type = character(0),
+    pie_locs = NULL
+  )
+  expect_equal(
+    exp_sig,
+    annotation_combinations(expected_significant_annotations)
+  )
 })

vignettes/gsea.Rmd

@@ -10,7 +10,7 @@ editor_options:
 <!--
 % \VignetteEngine{knitr::rmarkdown}
 % \VignetteIndexEntry{Gene Set Enrichment Analysis}
-% \VignetteDepends{categoryCompare2, GO.db, affy, hgu95av2.db, genefilter, estrogen, limma, Cairo, hgu95av2cdf, fgsea, data.table}
+% \VignetteDepends{categoryCompare2, GO.db, affy, hgu95av2.db, genefilter, estrogen, limma, ragg, hgu95av2cdf, fgsea, data.table}
 % \VignetteKeyword{categoryCompare, meta-analysis, gene ontology, kegg}
 % \VignettePackage{categoryCompare2}
 -->

vignettes/v2_guide.Rmd

@@ -10,7 +10,7 @@ editor_options:
 <!--
 % \VignetteEngine{knitr::rmarkdown}
 % \VignetteIndexEntry{categoryCompare: High-throughput data meta-analysis using gene annotations, V2}
-% \VignetteDepends{categoryCompare2, GO.db, affy, hgu95av2.db, genefilter, estrogen, limma, Cairo, hgu95av2cdf}
+% \VignetteDepends{categoryCompare2, GO.db, affy, hgu95av2.db, genefilter, estrogen, limma, ragg, hgu95av2cdf}
 % \VignetteKeyword{categoryCompare, meta-analysis, gene ontology, kegg}
 % \VignettePackage{categoryCompare2}
 -->