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add version parameter to R Package (#46)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,86 +1,92 @@ | ||
| #' @importFrom httr POST content | ||
| #' @importFrom readr read_tsv cols | ||
| #' @importFrom jsonlite toJSON | ||
| WebGestaltRNta <- function(organism="hsapiens", network="network_PPI_BIOGRID", method="Network_Retrieval_Prioritization", inputSeed, inputSeedFile, interestGeneType="genesymbol", neighborNum=10, highlightSeedNum=10, sigMethod="fdr", fdrThr=0.05, topThr=10, highlightType="Seeds", outputDirectory=getwd(), projectName=NULL, cache=NULL, hostName="https://www.webgestalt.org/") { | ||
| projectDir <- file.path(outputDirectory, paste0("Project_", projectName)) | ||
| # if (network == "network_FunMap") { | ||
| # network <- "network_FunMap_DenseModules" | ||
| # } | ||
| dir.create(projectDir) | ||
| WebGestaltRNta <- function(organism = "hsapiens", network = "network_PPI_BIOGRID", method = "Network_Retrieval_Prioritization", inputSeed, inputSeedFile, interestGeneType = "genesymbol", neighborNum = 10, highlightSeedNum = 10, sigMethod = "fdr", fdrThr = 0.05, topThr = 10, highlightType = "Seeds", outputDirectory = getwd(), projectName = NULL, cache = NULL, hostName = "https://www.webgestalt.org/") { | ||
| projectDir <- file.path(outputDirectory, paste0("Project_", projectName)) | ||
| # if (network == "network_FunMap") { | ||
| # network <- "network_FunMap_DenseModules" | ||
| # } | ||
| dir.create(projectDir) | ||
|
|
||
| if (length(network) > 1) { | ||
| stop("NTA does not support multiple databases.") | ||
| } | ||
| inputGene <- formatCheck("list", inputGeneFile=inputSeedFile, inputGene=inputSeed) | ||
| # only networks are in gene symbols | ||
| # mapping always returns gene symbol, could map to genesymbol but takes two requests | ||
| inputGene <- idMappingGene(organism=organism, dataType="list", inputGene=inputGene, sourceIdType=interestGeneType, targetIdType="entrezgene", mappingOutput=FALSE, hostName=hostName) | ||
| inputGene <- inputGene$mapped$geneSymbol | ||
|
|
||
| if (length(network) > 1) { | ||
| stop("NTA does not support multiple databases.") | ||
| } | ||
| inputGene <- formatCheck("list", inputGeneFile = inputSeedFile, inputGene = inputSeed) | ||
| # only networks are in gene symbols | ||
| # mapping always returns gene symbol, could map to genesymbol but takes two requests | ||
| inputGene <- idMappingGene(organism = organism, dataType = "list", inputGene = inputGene, sourceIdType = interestGeneType, targetIdType = "entrezgene", mappingOutput = FALSE, hostName = hostName) | ||
| inputGene <- inputGene$mapped$geneSymbol | ||
|
|
||
| if (startsWith(hostName, "file://")) { | ||
| dagInfo <- read_tsv( | ||
| removeFileProtocol(file.path(hostName, "geneset", paste(organism, "geneontology_Biological_Process", "entrezgene.dag", sep="_"))), | ||
| col_names=c("source", "target"), col_types="cc" | ||
| ) | ||
| } else { | ||
| geneSetUrl <- file.path(hostName, "api", "geneset") | ||
| response <- cacheUrl(geneSetUrl, cache=cache, query=list(organism=organism, database="geneontology_Biological_Process", standardId="entrezgene", fileType="dag")) | ||
| dagInfo <- read_tsv(content(response), col_names=c("source", "target"), col_types="cc") | ||
| } | ||
|
|
||
| ## networks <- unlist(strsplit(network, ",", fixed=TRUE)) | ||
| ## May need to bring back analysis of multiple networks | ||
| fileName <- paste(projectName, network, method, sep=".") | ||
| goEnrichRes <- randomWalkEnrichment(organism=organism, network=network, method=method, highlightSeedNum=highlightSeedNum, inputSeed=inputGene, | ||
| sigMethod=sigMethod, fdrThr=fdrThr, topThr=topThr, projectDir=projectDir, | ||
| topRank=neighborNum, projectName=projectName, cache=cache, hostName=hostName) | ||
| if (is.null(goEnrichRes)) { | ||
| return(NULL) | ||
| } | ||
| enrichResFile <- file.path(projectDir, paste0(fileName, "_enrichedResult.txt")) | ||
| if (startsWith(hostName, "file://")) { | ||
| dagInfo <- read_tsv( | ||
| removeFileProtocol(file.path(hostName, "geneset", paste(organism, "geneontology_Biological_Process", "entrezgene.dag", sep = "_"))), | ||
| col_names = c("source", "target"), col_types = "cc" | ||
| ) | ||
| } else { | ||
| geneSetUrl <- file.path(hostName, "api", "geneset") | ||
| response <- cacheUrl(geneSetUrl, cache = cache, query = list(organism = organism, database = "geneontology_Biological_Process", standardId = "entrezgene", fileType = "dag")) | ||
| dagInfo <- read_tsv(content(response), col_names = c("source", "target"), col_types = "cc") | ||
| } | ||
|
|
||
| goTermList <- read_tsv(enrichResFile, col_types=cols())$goId | ||
| inputEndIndex <- length(goTermList) | ||
| ## networks <- unlist(strsplit(network, ",", fixed=TRUE)) | ||
| ## May need to bring back analysis of multiple networks | ||
| fileName <- paste(projectName, network, method, sep = ".") | ||
| goEnrichRes <- randomWalkEnrichment( | ||
| organism = organism, network = network, method = method, highlightSeedNum = highlightSeedNum, inputSeed = inputGene, | ||
| sigMethod = sigMethod, fdrThr = fdrThr, topThr = topThr, projectDir = projectDir, | ||
| topRank = neighborNum, projectName = projectName, cache = cache, hostName = hostName | ||
| ) | ||
| if (is.null(goEnrichRes)) { | ||
| return(NULL) | ||
| } | ||
| enrichResFile <- file.path(projectDir, paste0(fileName, "_enrichedResult.txt")) | ||
|
|
||
| dagTree <- expandDag(goTermList, dagInfo) | ||
| goTermList <- dagTree$allNodes | ||
| edges <- dagTree$edges | ||
| rm(dagTree) | ||
| goTermList <- read_tsv(enrichResFile, col_types = cols())$goId | ||
| inputEndIndex <- length(goTermList) | ||
|
|
||
| if (startsWith(hostName, "file://")) { | ||
| goId2Term <- read_tsv( | ||
| removeFileProtocol(file.path(hostName, "geneset", paste(organism, "geneontology_Biological_Process", "entrezgene.des", sep="_"))), | ||
| col_names=c("id", "name"), col_types="cc" | ||
| ) | ||
| } else { | ||
| response <- POST(geneSetUrl, body=list(organism=organism, database="geneontology_Biological_Process", | ||
| fileType="des", ids=goTermList), encode="json") | ||
| goId2Term <- read_tsv(content(response), col_names=c("id", "name"), col_types="cc") | ||
| } | ||
| dagTree <- expandDag(goTermList, dagInfo) | ||
| goTermList <- dagTree$allNodes | ||
| edges <- dagTree$edges | ||
| rm(dagTree) | ||
|
|
||
| jsonFile <- file.path(projectDir, paste0(fileName, ".json")); | ||
| jsonData <- vector(mode="list", length=length(goTermList)) | ||
| if (startsWith(hostName, "file://")) { | ||
| goId2Term <- read_tsv( | ||
| removeFileProtocol(file.path(hostName, "geneset", paste(organism, "geneontology_Biological_Process", "entrezgene.des", sep = "_"))), | ||
| col_names = c("id", "name"), col_types = "cc" | ||
| ) | ||
| } else { | ||
| response <- POST(geneSetUrl, body = list( | ||
| organism = organism, database = "geneontology_Biological_Process", | ||
| fileType = "des", ids = goTermList, version = "2024" | ||
| ), encode = "json") | ||
| goId2Term <- read_tsv(content(response), col_names = c("id", "name"), col_types = "cc") | ||
| } | ||
|
|
||
| for (i in 1:length(goTermList)) { | ||
| goId <- goTermList[[i]] | ||
| goName <- filter(goId2Term, .data$id == goId)[[1, "name"]] | ||
| dataSets <- i <= inputEndIndex | ||
| jsonData[[i]] <- list(data=list(id=goId, name=goName, datasets=dataSets)) | ||
| } | ||
| jsonData <- unname(c(jsonData, edges)) | ||
| jsonFile <- file.path(projectDir, paste0(fileName, ".json")) | ||
| jsonData <- vector(mode = "list", length = length(goTermList)) | ||
|
|
||
| cat(toJSON(jsonData, auto_unbox=TRUE), "\n", sep="", file=jsonFile) | ||
| for (i in 1:length(goTermList)) { | ||
| goId <- goTermList[[i]] | ||
| goName <- filter(goId2Term, .data$id == goId)[[1, "name"]] | ||
| dataSets <- i <= inputEndIndex | ||
| jsonData[[i]] <- list(data = list(id = goId, name = goName, datasets = dataSets)) | ||
| } | ||
| jsonData <- unname(c(jsonData, edges)) | ||
|
|
||
| createNtaReport(networkName=network, method=method, sigMethod=sigMethod, fdrThr=fdrThr, topThr=topThr, | ||
| highlightType=highlightType, outputDirectory=outputDirectory, projectDir=projectDir, | ||
| projectName=projectName, hostName=hostName) | ||
| cat(toJSON(jsonData, auto_unbox = TRUE), "\n", sep = "", file = jsonFile) | ||
|
|
||
| cwd <- getwd() | ||
| setwd(projectDir) | ||
| zip(paste0(projectName, ".zip"), ".", flags="-rq") | ||
| setwd(cwd) | ||
| createNtaReport( | ||
| networkName = network, method = method, sigMethod = sigMethod, fdrThr = fdrThr, topThr = topThr, | ||
| highlightType = highlightType, outputDirectory = outputDirectory, projectDir = projectDir, | ||
| projectName = projectName, hostName = hostName | ||
| ) | ||
|
|
||
| cat("Results can be found in the ", projectDir, "!\n", sep="") | ||
| return(goEnrichRes) | ||
| cwd <- getwd() | ||
| setwd(projectDir) | ||
| zip(paste0(projectName, ".zip"), ".", flags = "-rq") | ||
| setwd(cwd) | ||
|
|
||
| cat("Results can be found in the ", projectDir, "!\n", sep = "") | ||
| return(goEnrichRes) | ||
| } |
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