在r包topgo里面绘制node图的函数是showSigOfNodes()，其中提供的第二个参数不能有0，否则会报错：

showSigOfNodes(sampleGOdata, score(resultKS.elim), firstSigNodes = 10, useInfo = "all") 
Error in if ((n <- as.integer(n[1L])) > 0) { : 
          missing value where TRUE/FALSE needed

showSigOfNodes()拆分之后是：

##sampleGOdata和score(resultKS.elim)是提供给函数的
        GOdata <- sampleGOdata
        
       # resultKS.elim <- runTest(sampleGOdata, algorithm = "elim", statistic = "ks")
        termsP.value <- score(resultKS.elim)
        tt <- sort(termsP.value)
        sigTerms <- tt[1:10]
        ###此处存在0因此后续会产生报错###
        
        baseNodes <- names(sigTerms)
        dag <- inducedGraph(graph(GOdata), baseNodes)
        dag <- reverseArch(dag)
        termCounts <- termStat(GOdata, nodes(dag))
        pval.info <- function(whichNodes) {
          ret.val <- format.pval(termsP.value[whichNodes], digits = 3, eps = 1e-20)
          names(ret.val) <- whichNodes
          return(ret.val)
        }
        library("DBI")
        .getTermsDefinition <- function(whichTerms, ontology, numChar = 20, multipLines = FALSE) {
          
          qTerms <- paste(paste("'", whichTerms, "'", sep = ""), collapse = ",")
          retVal <- dbGetQuery(GO_dbconn(), 
                               paste("SELECT term, go_id FROM go_term WHERE ontology IN",
                                                  "('", ontology, "') AND go_id IN (", qTerms, ");",
                                     sep = ""))
          
          termsNames <- retVal$term
          names(termsNames) <- retVal$go_id
          
          if(!multipLines)
            shortNames <- paste(substr(termsNames, 1, numChar),
                                ifelse(nchar(termsNames) > numChar, '...', ''), sep = '')
          else
            shortNames <- sapply(termsNames,
                                 function(x) {
                                   a <- strwrap(x, numChar)
                                   return(paste(a, sep = "", collapse = "\\\n"))
                                 })
          
          names(shortNames) <- names(termsNames)
          
          ## return NAs for the terms that are not found in the DB and make sure the 'names' attribute is as specified
          shortNames <- shortNames[whichTerms]
          names(shortNames) <- whichTerms
          
          return(shortNames)
        }

        .pval = pval.info(nodes(dag))
        .NO.CHAR=20
        .def = .getTermsDefinition(whichTerms = nodes(dag), ontology(GOdata), numChar = .NO.CHAR)
        .counts = apply(termCounts[, c("Significant", "Annotated")], 1, paste, collapse = " / ")
        nodeInfo <- paste(.def, .pval, .counts, sep = '\\\n')
        sigNodes <- sigTerms
        wantedNodes <- names(sigTerms)
        plotFunction = GOplot
        library("Rgraphviz")
        complete.dag <- plotFunction(dag, sigNodes = sigNodes, genNodes = names(sigTerms),
                                     wantedNodes = wantedNodes, showEdges = TRUE,
                                     useFullNames = T, oldSigNodes = NULL,
                                     nodeInfo = nodeInfo)
        # 绘图
        print(complete.dag)

修改之后：

 f <- function(x) {ifelse(x > 1e-17, x, 1e-17)} # 小于e-17都改成e-17
 showSigOfNodes(sampleGOdata, f(score(resultKS.elim)), firstSigNodes = 10, useInfo = "all")#计算的时候第二个参数改成f(score(resultKS.elim))