Support passing a GSON object to enrichMeSH(gson) and gseMeSH(gson)

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: meshes
 Title: MeSH Enrichment and Semantic analyses
-Version: 1.23.0
+Version: 1.23.0.991
 Authors@R: c( person(given = "Guangchuang", family = "Yu",        email = "[email protected]",   role = c("aut", "cre")),
               person(given = "Erqiang",     family = "Hu",        email = "[email protected]",       role = "ctb"))
 Description: MeSH (Medical Subject Headings) is the NLM controlled vocabulary
@@ -24,7 +24,8 @@ Imports:
     utils,
     AnnotationHub,
     MeSHDbi,
-    yulab.utils
+    yulab.utils,
+    gson
 Suggests:
     knitr,
     rmarkdown,
@@ -37,4 +38,4 @@ BugReports: https://github.com/GuangchuangYu/meshes/issues
 biocViews: Annotation, Clustering, MultipleComparison, Software
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0

NAMESPACE

@@ -9,6 +9,7 @@ export(geneInCategory)
 export(geneSim)
 export(gseMeSH)
 export(gseaplot)
+export(gson_mesh)
 export(heatplot)
 export(meshSim)
 export(meshdata)
@@ -32,8 +33,10 @@ importFrom(enrichplot,emapplot)
 importFrom(enrichplot,gseaplot)
 importFrom(enrichplot,heatplot)
 importFrom(enrichplot,ridgeplot)
+importFrom(gson,gson)
 importFrom(methods,new)
 importFrom(utils,packageDescription)
+importFrom(utils,stack)
 importFrom(yulab.utils,get_fun_from_pkg)
 importMethodsFrom(DOSE,show)
 importMethodsFrom(DOSE,summary)

NEWS.md

@@ -1,3 +1,6 @@
+# meshes 1.23.0.991
++ add `gson_mesh()` (2022-7-13, Wed)
+
 # meshes 1.19.3
 
 + cache mesh db and table (2021-09-01, Wed)

R/gson.R

@@ -0,0 +1,37 @@
+##' download the latest version of mesh data and stored in a 'GSON' object
+##'
+##'
+##' @title gson_Reactome
+##' @param MeSHDb MeSHDb
+##' @param database one of 'gendoo', 'gene2pubmed' or 'RBBH'
+##' @param category one of "A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L","M", "N", "V", "Z"
+##' @importFrom utils stack
+##' @importFrom gson gson
+##' @export
+gson_mesh <- function(MeSHDb, database, category) {
+
+    MeSH_DATA <- get_MeSH_data(MeSHDb, database, category) 
+    EXTID2PATHID = get("EXTID2PATHID", envir = MeSH_DATA)
+    PATHID2EXTID = get("PATHID2EXTID", envir = MeSH_DATA)
+    PATHID2NAME = get("PATHID2NAME", envir = MeSH_DATA) # NULL
+
+    reactomeAnno <- stack(PATHID2EXTID)   
+    gsid2gene <- reactomeAnno[, c(2,1)]
+    colnames(gsid2gene) <- c("gsid", "gene")
+    gsid2gene <- unique(gsid2gene[!is.na(gsid2gene[,2]), ]) 
+
+    termname <- PATHID2NAME
+    gsid2name <- NULL
+    if (is.null(termname)) {
+        gsid2name <- data.frame(gsid = names(termname), name = termname)
+    }
+
+    gson(gsid2gene = gsid2gene, 
+        gsid2name = gsid2name,
+        # species = species,
+        gsname = "MeSH",
+        # version = version,
+        accessed_date = as.character(Sys.Date())
+        # keytype = keytype
+    )
+}