Merge pull request #54 from bzhanglab/53-multi-list-ora-can-not-use-p…

…re-defined-reference-list fix(ora): add support for using pre-defined reference lists for multilist methods
bzhanglab · Aug 1, 2024 · e2bba4c · e2bba4c
2 parents beffc57 + 805553e
commit e2bba4c
Show file tree

Hide file tree

Showing 22 changed files with 308 additions and 239 deletions.
diff --git a/.lintr b/.lintr
@@ -1,7 +1,6 @@
 linters: linters_with_defaults(
     line_length_linter = NULL, 
     commented_code_linter = NULL,
-    no_tab_linter = NULL,
     object_name_linter = NULL
   )
 
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -23,9 +23,9 @@ Imports: methods, dplyr, doRNG, readr, parallel (>= 3.3.2),
         igraph, whisker, apcluster, Rcpp, cluster, poolr
 NeedsCompilation: yes
 LinkingTo: Rcpp
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 SystemRequirements: Cargo (Rust's package manager), rustc v1.63.0+
-Config/rextendr/version: 0.3.1
+Config/rextendr/version: 0.3.1.9000
 Config/WebGestaltR/MSRV: 1.63.0
 Encoding: UTF-8
 Suggests: 

diff --git a/R/WebGestaltRMultiOmics.R b/R/WebGestaltRMultiOmics.R
@@ -51,6 +51,13 @@
 #' @param referenceTypes Vector of the ID types of the reference lists. The supported ID types
 #'   of WebGestaltR for the selected organism can be found by the function \code{listIdType}.
 #'   If the \code{organism} is \code{others}, users do not need to set this parameter.
+#' @param referenceSets Users can directly select the reference sets from existing platforms in
+#'   WebGestaltR and do not need to provide the reference set through \code{referenceListFiles}.
+#'   All existing platforms supported in WebGestaltR can be found by the function
+#'   \code{listReferenceSets}. If \code{referenceListFiles} and \code{refereneceLists} are
+#'   \code{NULL}, WebGestaltR will use the \code{referenceSets} as the reference analyte sets.
+#'   Otherwise, WebGestaltR will use the user supplied reference set for enrichment analysis.
+#'   Must be a vector with length matching the input analyte list (i.e. c('genome', 'genome', 'KEGG'))
 #' @param minNum WebGestaltR will exclude the categories with the number of annotated genes
 #'   less than \code{minNum} for enrichment analysis. The default is \code{10}.
 #' @param maxNum WebGestaltR will exclude the categories with the number of annotated genes
@@ -99,7 +106,7 @@
 #' @param useWeightedSetCover Use weighted set cover for ORA. Defaults to \code{TRUE}.
 #' @param useAffinityPropagation Use affinity propagation for ORA. Defaults to \code{FALSE}.
 #' @param usekMedoid Use k-medoid for ORA. Defaults to \code{TRUE}.
-#' @param isMetaAnalysis whether to perform meta-analysis. Defaults to \code{TRUE}.
+#' @param isMetaAnalysis whether to perform meta-analysis. Defaults to \code{TRUE}. FALSE is not currently implemented.
 #' @param mergeMethod The method to merge the results from multiple omics (options: \code{mean}, \code{max}). Only used if \code{isMetaAnalysis = FALSE}. Defaults to \code{mean}.
 #' @param normalizationMethod The method to normalize the results from multiple omics (options: \code{rank}, \code{median}, \code{mean}). Only used if \code{isMetaAnalysis = FALSE}.
 #' @param kMedoid_k The number of clusters for k-medoid. Defaults to \code{25}.
@@ -112,7 +119,7 @@ WebGestaltRMultiOmics <- function(analyteLists = NULL, analyteListFiles = NULL,
                                   projectName = NULL, dagColor = "binary", saveRawGseaResult = FALSE, gseaPlotFormat = "png", nThreads = 1, cache = NULL,
                                   hostName = "https://www.webgestalt.org/", useWeightedSetCover = TRUE, useAffinityPropagation = FALSE,
                                   usekMedoid = FALSE, kMedoid_k = 25, isMetaAnalysis = TRUE, mergeMethod = "mean", normalizationMethod = "rank",
-                                  referenceLists = NULL, referenceListFiles = NULL, referenceTypes = NULL, listNames = NULL) {
+                                  referenceLists = NULL, referenceListFiles = NULL, referenceTypes = NULL, referenceSets = NULL, listNames = NULL) {
   VALID_MERGE_METHODS <- c("mean", "max")
   VALID_NORM_METHODS <- c("rank", "median", "mean")
   VALID_ENRICH_METHODS <- c("ORA", "GSEA")
@@ -126,6 +133,7 @@ WebGestaltRMultiOmics <- function(analyteLists = NULL, analyteListFiles = NULL,
     referenceLists <- testNull(referenceLists)
     referenceListFiles <- testNull(referenceListFiles)
     referenceTypes <- testNull(referenceTypes)
+    referenceSets <- testNull(referenceSets)
   }
   organism <- testNull(organism)
   enrichDatabase <- testNull(enrichDatabase)
@@ -193,7 +201,7 @@ WebGestaltRMultiOmics <- function(analyteLists = NULL, analyteListFiles = NULL,
       setCoverNum = setCoverNum, perNum = perNum, isOutput = isOutput, outputDirectory = outputDirectory, projectName = projectName,
       dagColor = dagColor, nThreads = nThreads, cache = cache, hostName = hostName, useWeightedSetCover = useWeightedSetCover,
       useAffinityPropagation = useAffinityPropagation, usekMedoid = usekMedoid, kMedoid_k = kMedoid_k, referenceLists = referenceLists,
-      referenceListFiles = referenceListFiles, referenceTypes = referenceTypes, listNames = listNames
+      referenceListFiles = referenceListFiles, referenceTypes = referenceTypes, referenceSets = referenceSets, listNames = listNames
     )
     ## Meta-analysis
   } else if (enrichMethod == "GSEA") {
@@ -266,18 +274,18 @@ WebGestaltRMultiOmics <- function(analyteLists = NULL, analyteListFiles = NULL,
   all_sets <- list(geneSet = list(), geneSetDes = list(), geneSetDag = list(), geneSetNet = list(), standardId = list(), databases = list())
   if (!is.null(enrichDatabase)) { # Need to get correct name for metabolite databases
     if (length(unique(analyteTypes)) == 1) {
-        db <- get_gmt_file(hostName, analyteTypes[1], enrichDatabase, organism, cache)
-        res <- loadGeneSet(
-          organism = organism, enrichDatabase = db, enrichDatabaseFile = enrichDatabaseFile, enrichDatabaseType = enrichDatabaseType,
-          enrichDatabaseDescriptionFile = enrichDatabaseDescriptionFile, cache = cache, hostName = hostName, isMultiOmics = FALSE
-        )
-        elements <- names(res)
-        for (i in seq_along(analyteTypes)) {
-          for (j in seq_along(elements)) {
-            all_sets[[elements[j]]][[i]] <- res[[elements[j]]]
-          }
-          all_sets$databases[[i]] <- db
+      db <- get_gmt_file(hostName, analyteTypes[1], enrichDatabase, organism, cache)
+      res <- loadGeneSet(
+        organism = organism, enrichDatabase = db, enrichDatabaseFile = enrichDatabaseFile, enrichDatabaseType = enrichDatabaseType,
+        enrichDatabaseDescriptionFile = enrichDatabaseDescriptionFile, cache = cache, hostName = hostName, isMultiOmics = FALSE
+      )
+      elements <- names(res)
+      for (i in seq_along(analyteTypes)) {
+        for (j in seq_along(elements)) {
+          all_sets[[elements[j]]][[i]] <- res[[elements[j]]]
         }
+        all_sets$databases[[i]] <- db
+      }
     } else {
       for (i in seq_along(analyteTypes)) {
         db <- get_gmt_file(hostName, analyteTypes[i], enrichDatabase, organism, cache)

diff --git a/R/WebGestaltRMultiomicsOra.R b/R/WebGestaltRMultiomicsOra.R
@@ -8,7 +8,7 @@ WebGestaltRMultiOmicsOra <- function(analyteLists = NULL, analyteListFiles = NUL
                                      topThr = 10, reportNum = 100, setCoverNum = 10, perNum = 1000, gseaP = 1, isOutput = TRUE, outputDirectory = getwd(),
                                      projectName = NULL, dagColor = "binary", nThreads = 1, cache = NULL, hostName = "https://www.webgestalt.org/",
                                      useWeightedSetCover = TRUE, useAffinityPropagation = FALSE, usekMedoid = FALSE, kMedoid_k = 25,
-                                     referenceLists = NULL, referenceListFiles = NULL, referenceTypes = NULL, listNames = NULL) {
+                                     referenceLists = NULL, referenceListFiles = NULL, referenceTypes = NULL, referenceSets = NULL, listNames = NULL) {
   projectDir <- file.path(outputDirectory, paste0("Project_", projectName))
   cat("Performing multi-omics ORA\nLoading the functional categories...\n")
   all_sets <- .load_meta_gmt(enrichDatabase, enrichDatabaseFile, enrichDatabaseDescriptionFile, enrichDatabaseType, analyteLists, analyteListFiles, analyteTypes, organism, cache, hostName)
@@ -53,7 +53,7 @@ WebGestaltRMultiOmicsOra <- function(analyteLists = NULL, analyteListFiles = NUL
 
   cat("Loading the reference lists...\n")
   reference_lists <- list()
-  if (is.null(referenceLists)) {
+  if (!is.null(referenceListFiles)) {
     for (i in seq_along(referenceListFiles)) {
       referenceGeneList <- loadReferenceGene(
         organism = organism, referenceGeneFile = referenceListFiles[i],
@@ -65,7 +65,7 @@ WebGestaltRMultiOmicsOra <- function(analyteLists = NULL, analyteListFiles = NUL
       )
       reference_lists[[i]] <- referenceGeneList
     }
-  } else {
+  } else if (!is.null(referenceLists)) {
     for (i in seq_along(analyteLists)) {
       referenceGeneList <- loadReferenceGene(
         organism = organism, referenceGeneFile = NULL,
@@ -77,6 +77,18 @@ WebGestaltRMultiOmicsOra <- function(analyteLists = NULL, analyteListFiles = NUL
       )
       reference_lists[[i]] <- referenceGeneList
     }
+  } else { # use pre-defined reference lists
+    for (i in seq_along(interest_lists)) {
+      referenceGeneList <- loadReferenceGene(
+        organism = organism, referenceGeneFile = NULL,
+        referenceGene = NULL, referenceGeneType = NULL,
+        referenceSet = referenceSets[[i]], collapseMethod = collapseMethod,
+        hostName = hostName, geneSet = all_sets[["geneSet"]][[i]],
+        interestGeneList = interest_lists[[i]],
+        cache = cache
+      )
+      reference_lists[[i]] <- referenceGeneList
+    }
   }
   cat("Running multi-omics ORA...\n")
   oraRes <- multiOraEnrichment(interest_lists, reference_lists, all_sets[["geneSet"]],
@@ -283,7 +295,7 @@ WebGestaltRMultiOmicsOra <- function(analyteLists = NULL, analyteListFiles = NUL
       interestGeneFile_list = analyteListFiles, interestGene_list = interest_lists,
       interestGeneType_list = analyteTypes, collapseMethod = collapseMethod,
       referenceGeneFile_list = referenceListFiles, referenceGene_list = referenceLists,
-      referenceGeneType_list = referenceTypes, referenceSet_list = referenceLists, minNum = minNum,
+      referenceGeneType_list = referenceTypes, referenceSet_list = referenceSets, minNum = minNum,
       maxNum = maxNum, fdrMethod = fdrMethod, sigMethod = sigMethod, fdrThr = fdrThr,
       topThr = topThr, reportNum = reportNum, dagColor = dagColor, listNames = listNames
     )

diff --git a/R/WebGestaltRNta.R b/R/WebGestaltRNta.R
@@ -58,7 +58,7 @@ WebGestaltRNta <- function(organism = "hsapiens", network = "network_PPI_BIOGRID
     } else {
         response <- POST(geneSetUrl, body = list(
             organism = organism, database = "geneontology_Biological_Process",
-            fileType = "des", ids = goTermList, version = "2024"
+            fileType = "des", ids = goTermList, version = WEBGESTALT_DATA_VERSION
         ), encode = "json")
         goId2Term <- read_tsv(content(response), col_names = c("id", "name"), col_types = "cc")
     }

diff --git a/R/cacheFile.R b/R/cacheFile.R
@@ -38,11 +38,11 @@ cacheUrl <- function(dataUrl, cache = NULL, query = NULL) {
         # cat("Reading from server: ", dataUrl, "\n")
         if (!is.null(query)) {
             if (!("version" %in% names(query))) {
-                query[["version"]] <- "2024"
+                query[["version"]] <- WEBGESTALT_DATA_VERSION
             }
             response <- GET(dataUrl, query = query)
         } else {
-            response <- GET(dataUrl, query = list(version = "2024"))
+            response <- GET(dataUrl, query = list(version = WEBGESTALT_DATA_VERSION))
         }
         if (response$status_code != 200) {
             return(response)

diff --git a/R/constants.R b/R/constants.R
@@ -0,0 +1 @@
+WEBGESTALT_DATA_VERSION <- "2024"
diff --git a/R/extendr-wrappers.R b/R/extendr-wrappers.R
@@ -6,7 +6,6 @@
 # This file was created with the following call:
 #   .Call("wrap__make_WebGestaltR_wrappers", use_symbols = TRUE, package_name = "WebGestaltR")
 
-#' @docType package
 #' @usage NULL
 #' @useDynLib WebGestaltR, .registration = TRUE
 NULL