Deleted enrichmbKEGG function

.Rbuildignore

@@ -13,3 +13,5 @@ docs
 .github
 site_src
 TODO.md
+^.*\.Rproj$
+^\.Rproj\.user$

.Rhistory

@@ -0,0 +1,133 @@
+install.packages("ggplot2")
+if (!requireNamespace("BiocManager", quietly = TRUE))
+install.packages("BiocManager")
+BiocManager::install("clusterProfiler")
+library(ggplot2)
+library(clusterProfiler)
+BiocManager::install("clusterProfiler")
+BiocManager::install("MicrobiotaProcess")
+install.packages("VennDiagram")
+library(VennDiagram)
+nifW.out <- read.table(file = "/mnt/e/SMU/Projects/Genepredict/data/hmmbuild_hmmfiles/nifW_NCyc_idv2.txt", header = F)
+nifW.out <- read.table(file = "E:/SMU/Projects/Genepredict/data/hmmbuild_hmmfiles/nifW_NCyc_idv2.txt", header = F)
+View(nifW.out)
+View(nifW.out)
+View(nifW.out)
+View(nifW.out)
+nifK.out <- read.table(file = "E:/SMU/Projects/Genepredict/data/hmmbuild_hmmfiles/nifK_NCyc_idv2.txt", header = F)
+nifD.out <- read.table(file = "E:/SMU/Projects/Genepredict/data/hmmbuild_hmmfiles/nifD_NCyc_idv2.txt", header = F)
+nifW.in <- read.table(file = "E:/SMU/Projects/Genepredict/data/NCycDB/data/NCyc_100_2019Jul/nifW.NCyc.txt")
+nifK.in <- read.table(file = "E:/SMU/Projects/Genepredict/data/NCycDB/data/NCyc_100_2019Jul/nifK.NCyc.txt")
+nifD.in <- read.table(file = "E:/SMU/Projects/Genepredict/data/NCycDB/data/NCyc_100_2019Jul/nifD.NCyc.txt")
+venn.diagram(x=list(hmmfiles=nifD.in, NCycdb=nifD.out), "nifW.png", height = 450, width = 450, resolution =300,
+imagetype="png", col="white", fill=c(colors()[616], colors()[38]),
+alpha=c(0.6, 0.6), lwd=c(1, 1), cex=0, cat.dist=c(-0.07, -0.07, -0.05), cat.pos=c(300, 60, 180),
+cat.cex=0.45)
+venn.diagram(x=list(hmmfiles=nifD.in, NCycdb=nifD.out), "nifW.png", height = 450, width = 450, resolution =300,
+imagetype="png", col="white", fill=c(colors()[616], colors()[38]),
+alpha=c(0.6, 0.6), lwd=c(1, 1), cex=0)
+View(nifD.in)
+View(nifD.out)
+x <- sample(1:10,1)
+x
+x <- sample(1:10,1)
+x
+x <- sample(1:100,1)
+x
+x <- sample(1:100,1)
+x
+sample(1:100,1)
+sample(1:100,1)
+sample(1:100,1)
+sample(1:100,1)
+sample(1:100,1)
+x <- sample(1:100,1)
+x
+x <- sample(1:100,1)
+x
+ll
+update.packages()
+setwd("D:/yulab/clusterProfiler")
+#'
+#' @return A gene annotation table of  human gut microbiome
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' getM_DATA(hgmlist)
+#' }
+#'
+#'
+getM_DATA <- function(Kgenelist){
+p <- kegg_list('pathway')
+p2 <- kegg_link('ko',"pathway")
+p2 <- p2[grep(pattern="path:map",p2[,1]),]
+res <- merge(p2, p, by = 'from', all.x=TRUE)
+colnames(res) <- c("pathway", "Knum", "name")
+res$Knum <- gsub("ko:","",res$Knum)
+M_DATA <- res[res[,2] %in% Kgenelist,]
+return(M_DATA)
+}
+#' @return A \code{enrichResult} instance.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' data(hgmlist)
+#' yy <- enrichmbKEGG(hgmlist[1:20],microbe_data=hgmlist)
+#' }
+#'
+#'
+enrichmbKEGG <- function(gene,
+pvalueCutoff      = 0.05,
+pAdjustMethod     = "BH",
+universe,
+minGSSize         = 10,
+maxGSSize         = 500,
+qvalueCutoff      = 0.2,
+use_internal_data = FALSE,
+microbe_data) {
+M_DATA <- getM_DATA(microbe_data)
+KEGG_DATA <- build_Anno(M_DATA[c(c("pathway","Knum"))], M_DATA[c("pathway","name")])
+res <- enricher_internal(gene,
+pvalueCutoff  = pvalueCutoff,
+pAdjustMethod = pAdjustMethod,
+universe      = universe,
+minGSSize     = minGSSize,
+maxGSSize     = maxGSSize,
+qvalueCutoff  = qvalueCutoff,
+USER_DATA = KEGG_DATA)
+if (is.null(res))
+return(res)
+res@ontology <- "KEGG"
+res@organism <- "microbiome"
+return(res)
+}
+setwd("E:/SMU/Projects/FunctionalAnnoforMGS/2_functionalannformgs/8_hgmKO")
+nbt_hgm <- read.table(file = "E:/SMU/Projects/FunctionalAnnoforMGS/2_functionalannformgs/8_hgmKO/NBT_6980KOs_for_humangutmetagenome.txt", header = T, sep = "\t",quote ="", fill = T)
+library(clusterProfiler)
+library(DOSE)
+ko2path <- read.table(file = "NBT_HGM_KO2PATHWAY.txt",header = T,sep = "\t")
+data <- read.delim(file = "E:/SMU/Projects/test/IBS.txt",stringsAsFactors=FALSE,header = T,row.names = 1)
+genelist <- rownames(data)
+kk2 <- enrichKEGG(genelist[101:200],organism = "ko")
+genelist <- rownames(data)
+kk <- enricher(gene = genelist[101:200],
+pvalueCutoff = 0.05,
+pAdjustMethod = "BH",
+minGSSize = 10,
+maxGSSize = 500,
+qvalueCutoff =0.05,
+TERM2GENE = ko2path[c("pathway","KO")],
+TERM2NAME = ko2path[c("pathway","description")])
+dotplot(kk)
+#kk2 <- enrichKEGG(genelist[101:200],organism = "ko")
+kk3 <- enrichKEGG(genelist[101:200],organism = "ko",universe = ko2path$KO)
+dotplot(kk3)
+setwd("D:/yulab/clusterProfiler")
+data(hgmlist)
+kk <- enrichKEGG(gene = hgmlist[1:20], organism = "ko", universe = hgmlist )
+dotplot(kk)
+kk2 <- enrichKEGG(gene = hgmlist[1:20], organism = "ko")
+dotplot(kk2)
+setwd("D:/yulab/clusterProfiler")

.gitignore

@@ -6,3 +6,4 @@ vignettes/.DS_Store
 __pycache__
 __init__.py
 __init__.pyc
+.Rproj.user

NAMESPACE

@@ -54,11 +54,9 @@ export(enrichKEGG)
 export(enrichMKEGG)
 export(enrichWP)
 export(enricher)
-export(enrichmbKEGG)
 export(filter)
 export(geneID)
 export(geneInCategory)
-export(getM_DATA)
 export(get_wp_organisms)
 export(go2ont)
 export(go2term)

clusterProfiler.Rproj

@@ -0,0 +1,21 @@
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 4
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace