update

YuLab-SMU · Jul 26, 2024 · f205795 · f205795
1 parent e16f9e0
commit f205795
Show file tree

Hide file tree

Showing 7 changed files with 86 additions and 47 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clusterProfiler
 Type: Package
 Title: A universal enrichment tool for interpreting omics data
-Version: 4.13.0
+Version: 4.13.0.001
 Authors@R: c(
     person(given = "Guangchuang", family = "Yu",        email = "[email protected]",   role  = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),
     person(given = "Li-Gen",      family = "Wang",      email = "[email protected]",   role  = "ctb"),
@@ -17,7 +17,6 @@ Depends:
     R (>= 3.5.0)
 Imports:
     AnnotationDbi,
-    downloader,
     DOSE (>= 3.23.2),
     dplyr,
     enrichplot (>= 1.9.3),
@@ -54,4 +53,4 @@ Packaged: NA
 biocViews: Annotation, Clustering, GeneSetEnrichment, GO, KEGG,
     MultipleComparison, Pathways, Reactome, Visualization
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,4 @@
-# clusterProfiler 4.12.0
 
-+ Bioconductor RELEASE_3_19 (2024-05-15, Wed)
 
 <!--
 
@@ -14,6 +12,21 @@ TODO:
   - e.g. independent test for different omics data and then combine results
 -->
 
+# clusterProfiler 4.13.0.001
+
++ update `kegg_category` information (7 categories and 572 subcategories) (2024-07-26, Fri)
+  - Cellular Processes (36)                    
+  - Drug Development (75)
+  - Environmental Information Processing (41)
+  - Genetic Information Processing (39)
+  - Human Diseases (99)
+  - Metabolism (190)
+  - Organismal Systems (92)
+
+# clusterProfiler 4.12.0
+
++ Bioconductor RELEASE_3_19 (2024-05-15, Wed)
+
 # clusterProfiler 4.10.1
 
 + bug fixed in parsing KEGG category (2024-03-07, Thu, #664)

diff --git a/R/utilities.R b/R/utilities.R
@@ -1,19 +1,19 @@
 
-# the `read_with_cache` is a better solution
-mydownload <- function(url, method = NULL, quiet = TRUE, ...) {
-    if (is.null(method))
-        method <- getOption("clusterProfiler.download.method")
-
-    if (!is.null(method) && method != "auto") { 
-        dl <- tryCatch(utils::download.file(url, quiet = TRUE, method = method, ...),
-                       error = function(e) NULL)       
-    } else {
-        dl <- tryCatch(downloader::download(url, quiet = TRUE, ...),
-                       error = function(e) NULL)        
-    }
-
-    return(dl)
-}
+# # the `yread` is a better solution
+# mydownload <- function(url, method = NULL, quiet = TRUE, ...) {
+#     if (is.null(method))
+#         method <- getOption("clusterProfiler.download.method")
+
+#     if (!is.null(method) && method != "auto") { 
+#         dl <- tryCatch(utils::download.file(url, quiet = TRUE, method = method, ...),
+#                        error = function(e) NULL)       
+#     } else {
+#         dl <- tryCatch(downloader::download(url, quiet = TRUE, ...),
+#                        error = function(e) NULL)        
+#     }
+
+#     return(dl)
+# }
 
 
 

diff --git a/R/zzz.R b/R/zzz.R
@@ -1,32 +1,35 @@
 ##' @importFrom utils packageDescription
 .onAttach <- function(libname, pkgname) {
-    pkgVersion <- packageDescription(pkgname, fields="Version")
-    msg <- paste0(pkgname, " v", pkgVersion, "  ",
-                  "For help: https://yulab-smu.top/biomedical-knowledge-mining-book/", "\n\n")
-
-    if (.Platform$OS.type == "windows") {
-        dl.method <- "wininet"
-    } else if (capabilities("libcurl")) {
-        dl.method <- "libcurl"
-    } else {
-        dl.method <- getOption("download.file.method", default = "auto") 
-    }
+    # pkgVersion <- packageDescription(pkgname, fields="Version")
+    # msg <- paste0(pkgname, " v", pkgVersion, "  ",
+    #               "For help: https://yulab-smu.top/biomedical-knowledge-mining-book/", "\n\n")
+
+    # if (.Platform$OS.type == "windows") {
+    #     dl.method <- "wininet"
+    # } else if (capabilities("libcurl")) {
+    #     dl.method <- "libcurl"
+    # } else {
+    #     dl.method <- getOption("download.file.method", default = "auto") 
+    # }
+
+    # options(clusterProfiler.download.method = dl.method)
+    # options(timeout = max(300, getOption("timeout"))) # see ?download.file
 
 
     # Define a cache directory
     options(clusterProfiler_cache_dir = tempdir())
 
-    options(clusterProfiler.download.method = dl.method)
-    options(timeout = max(300, getOption("timeout"))) # see ?download.file
 
-    citation <- paste0("If you use ", pkgname, " in published research, please cite:\n",
-                       "T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, ",
-                       "W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. ", 
-                       "clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. ", 
-                       "The Innovation. 2021, 2(3):100141")
+    # citation <- paste0("If you use ", pkgname, " in published research, please cite:\n",
+    #                    "T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, ",
+    #                    "W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. ", 
+    #                    "clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. ", 
+    #                    "The Innovation. 2021, 2(3):100141")
 
 
-    packageStartupMessage(paste0(msg, citation))
+    # packageStartupMessage(paste0(msg, citation))
+
+    packageStartupMessage(yulab.utils::yulab_msg(pkgname))
 }
 
 
diff --git a/data/kegg_category.rda b/data/kegg_category.rda
diff --git a/inst/CITATION b/inst/CITATION
@@ -1,6 +1,36 @@
 citHeader("Please cite T. Wu (2021) for using clusterProfiler. In addition, please cite G. Yu (2010) when using GOSemSim, G. Yu (2015) when using DOSE and G. Yu (2015) when using ChIPseeker.")
 
 
+refs <- yulab.utils:::ref_knowledge()
+
+citEntry(entry  ="ARTICLE",
+	    title = "Using clusterProfiler to characterize multiomics data",
+	    author = c(
+            person("Shuangbin", "Xu"),
+            person("Erqiang", "Hu"),
+            person("Yantong", "Cai"),
+            person("Zijing", "Xie"),
+            person("Xiao", "Luo"),
+            person("Li", "Zhan"),
+            person("Wenli", "Tang"),
+            person("Qianwen", "Wang"),
+            person("Bingdong", "Liu"),
+            person("Rui", "Wang"),
+            person("Wenqin", "Xie"),
+            person("Tianzhi", "Wu"),
+            person("Liwei", "Xie"),
+            person("Guangchuang", "Yu")
+            ),
+    	issn = "1750-2799",
+	    url = "https://www.nature.com/articles/s41596-024-01020-z",
+    	doi = "10.1038/s41596-024-01020-z",
+    	journal = "Nature Protocols",
+    	month = "Jul",
+	    year = "2024",
+    	pages = "",
+        textVersion = refs['clusterProfiler_NP']
+)
+
 citEntry(entry  ="ARTICLE",
          title  = "clusterProfiler 4.0: A universal enrichment tool for interpreting omics data",
          author = c(
@@ -26,10 +56,7 @@ citEntry(entry  ="ARTICLE",
          pages   = "100141",
          PMID    = "",
          doi     = "10.1016/j.xinn.2021.100141",
-         textVersion = paste("T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou,",
-                             "W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu.", 
-                             "clusterProfiler 4.0: A universal enrichment tool for interpreting omics data.", 
-                             "The Innovation. 2021, 2(3):100141")
+         textVersion = refs['clusterProfiler_Innovation']
          )
 
 citEntry(entry  ="ARTICLE",
@@ -47,7 +74,5 @@ citEntry(entry  ="ARTICLE",
          pages   = "284-287",
          PMID    = "22455463",
          doi     = "10.1089/omi.2011.0118",
-         textVersion = paste("Guangchuang Yu, Li-Gen Wang, Yanyan Han and Qing-Yu He.",
-             "clusterProfiler: an R package for comparing biological themes among gene clusters.",
-             "OMICS: A Journal of Integrative Biology 2012, 16(5):284-287")
+         textVersion = refs['clusterProfiler']
          )
diff --git a/man/clusterProfiler-package.Rd b/man/clusterProfiler-package.Rd