Fix/implement non hsa id conversion in get kegg gsets (#201)

* fix kegg id to symbol conversion in `get_kegg_gsets()`

* bump dev version

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pathfindR
 Type: Package
 Title: Enrichment Analysis Utilizing Active Subnetworks
-Version: 2.3.1.9001
+Version: 2.3.1.9002
 Authors@R: c(person("Ege", "Ulgen",
                     role = c("cre", "cph"), 
                     email = "[email protected]",

R/data_generation.R

@@ -174,28 +174,37 @@ get_kegg_gsets <- function(org_code = "hsa") {
 
   message("Grab a cup of coffee, this will take a while...")
 
-  url <- paste0("https://rest.kegg.jp/list/pathway/", org_code)
-  result <- httr::GET(url)
-  result <- httr::content(result, "text")
-
-  parsed_result <- strsplit(result, "\n")[[1]]
-  pathway_ids <- vapply(parsed_result, function(x) unlist(strsplit(x, "\t"))[1], "id")
-  pathway_descriptons <- vapply(parsed_result, function(x) unlist(strsplit(x, "\t"))[2], "description")
+  gene_table_url <- paste0("https://rest.kegg.jp/list/", org_code)
+  gene_table_result <- httr::GET(gene_table_url)
+  gene_table_result <- httr::content(gene_table_result, "text")
+
+  parsed_gene_table_result <- strsplit(gene_table_result, "\n")[[1]]
+  kegg_gene_table <- data.frame(
+    kegg_id = unname(vapply(parsed_gene_table_result, function(x) unlist(strsplit(x, "\t"))[1], "org:123")),
+    symbol = unname(vapply(parsed_gene_table_result, function(x) unlist(strsplit(unlist(strsplit(x, "\t"))[4], ";"))[1], "symbol"))
+  )
+  # remove mistaken lines
+  kegg_gene_table <- kegg_gene_table[grep("^((,\\s)?[A-Za-z0-9_-]+(\\@)?)+$", kegg_gene_table$symbol), ]
+
+
+  all_pathways_url <- paste0("https://rest.kegg.jp/list/pathway/", org_code)
+  all_pathways_result <- httr::GET(all_pathways_url)
+  all_pathways_result <- httr::content(all_pathways_result, "text")
+  parsed_all_pathways_result <- strsplit(all_pathways_result, "\n")[[1]]
+  pathway_ids <- vapply(parsed_all_pathways_result, function(x) unlist(strsplit(x, "\t"))[1], "id")
+  pathway_descriptons <- vapply(parsed_all_pathways_result, function(x) unlist(strsplit(x, "\t"))[2], "description")
   names(pathway_descriptons) <- pathway_ids
 
   genes_by_pathway <- lapply(pathway_ids, function(pw_id) {
     pathways_graph <- ggkegg::pathway(pid = pw_id, directory = tempdir(), use_cache = FALSE, return_tbl_graph = FALSE)
     all_pw_gene_ids <- igraph::V(pathways_graph)$name[igraph::V(pathways_graph)$type == "gene"]
     all_pw_gene_ids <- unlist(strsplit(all_pw_gene_ids, " "))
     all_pw_gene_ids <- unique(all_pw_gene_ids)
-    all_pw_gene_ids <- sub("^hsa:", "", all_pw_gene_ids)
-
-    all_pw_gene_symbols <- AnnotationDbi::mget(
-      all_pw_gene_ids, org.Hs.eg.db::org.Hs.egSYMBOL, ifnotfound = NA
-    )
 
-    all_pw_gene_symbols <- unique(unname(unlist(all_pw_gene_symbols)))
+    all_pw_gene_symbols <- kegg_gene_table$symbol[match(all_pw_gene_ids, kegg_gene_table$kegg_id)]
     all_pw_gene_symbols <- all_pw_gene_symbols[!is.na(all_pw_gene_symbols)]
+    all_pw_gene_symbols <- unname(vapply(all_pw_gene_symbols, function(x) unlist(strsplit(x, ", "))[1], "symbol"))
+    all_pw_gene_symbols <- unique(all_pw_gene_symbols)
 
     return(all_pw_gene_symbols)
   })

tests/testthat/test-data_generation.R

@@ -74,20 +74,35 @@ test_that("`gset_list_from_gmt()` -- works as expected", {
 
 test_that("`get_kegg_gsets()` -- works as expected", {
   skip_on_cran()
-  mock_content <- "hsa04972\tdescription\nhsa04962\tdescription2"
-  with_mock(`httr::content` = function(...) mock_content, {
-    expect_is(hsa_kegg <- pathfindR:::get_kegg_gsets(), "list")
+  mock_responses <- c(
+    httr::content(httr::GET(paste0("https://rest.kegg.jp/list/eco")), "text"),
+    "eco00010\tdescription\neco00071\tdescription2"
+  )
+
+  call_count <- 0
+
+  # function to manage sequential responses
+  mock_content <- function(...) {
+    call_count <<- call_count + 1
+    return(mock_responses[call_count])
+  }
+
+
+  with_mock(`httr::content` = mock_content, {
+    expect_is(toy_eco_kegg <- pathfindR:::get_kegg_gsets(), "list")
   })
 
-  expect_length(hsa_kegg, 2)
-  expect_true(all(names(hsa_kegg) == c("gene_sets", "descriptions")))
-  expect_true(all(names(hsa_kegg[["gene_sets"]]) %in% names(hsa_kegg[["descriptions"]])))
+  expect_length(toy_eco_kegg, 2)
+  expect_true(all(names(toy_eco_kegg) == c("gene_sets", "descriptions")))
+  expect_true(all(names(toy_eco_kegg[["gene_sets"]]) %in% names(toy_eco_kegg[["descriptions"]])))
+  expect_length(toy_eco_kegg[["gene_sets"]], 2)
+  expect_length(toy_eco_kegg[["descriptions"]], 2)
 
-  expect_true(hsa_kegg[["descriptions"]]["hsa04972"] == "description")
-  expect_true(hsa_kegg[["descriptions"]]["hsa04962"] == "description2")
+  expect_true(toy_eco_kegg[["descriptions"]]["eco00010"] == "description")
+  expect_true(toy_eco_kegg[["descriptions"]]["eco00071"] == "description2")
 
-  expect_length(hsa_kegg[["gene_sets"]][["hsa04972"]], 102)
-  expect_length(hsa_kegg[["gene_sets"]][["hsa04962"]], 44)
+  expect_length(toy_eco_kegg[["gene_sets"]][["eco00010"]], 47)
+  expect_length(toy_eco_kegg[["gene_sets"]][["eco00071"]], 15)
 })
 
 test_that("`get_reactome_gsets()` -- works as expected", {