update data

Author: Ziwei-Huang-BU

.DS_Store

@@ -260,3 +260,58 @@
 #' Bioinformatics 36.4 (2020): 1307-1308.
 #'
 "reactome"
+
+#' hypeR-GEM object of age-associated metabolites obtained from New England Centenarian Study (NECS)
+#'
+#' A a list object
+#'
+#' @docType data
+#'
+#' @usage data(hypeR_object_NECS)
+#'
+#' @format a list object
+#'
+#' @return a list object
+#'
+#' @references TBD
+#'
+#'
+#'
+"hypeR_object_NECS"
+
+
+#' A list of enriched Metabolon-based metabolite sets (MSets) obtained from age-associated metabolites in NECS
+#'
+#' A a list object
+#'
+#' @docType data
+#'
+#' @usage data(metabolon_msets_list)
+#'
+#' @format a list object
+#'
+#' @return a list object
+#'
+#' @references Evans, A. M., DeHaven, C. D., Barrett, T., Mitchell, M. & Milgram, E.
+#' Integrated, Nontargeted Ultrahigh Performance Liquid Chromatography/Electrospray Ionization
+#' Tandem Mass Spectrometry Platform for the Identification and Relative Quantification of
+#' the Small-Molecule Complement of Biological Systems. Anal. Chem. 81, 6656–6667 (2009).
+"metabolon_msets_list"
+
+#' A list of enriched gene-sets in HALLMARK,KEGG, and REACTOME derived from "hypeR_object_NECS"
+#'
+#' A a list object
+#'
+#' @docType data
+#'
+#' @usage data(gsets_list)
+#'
+#' @format a list object
+#'
+#' @return a list object
+#'
+#' @references Federico, Anthony, and Stefano Monti.
+#' "hypeR: an R package for geneset enrichment workflows."
+#' Bioinformatics 36.4 (2020): 1307-1308.
+#'
+"gsets_list"

R/data.R

@@ -220,13 +220,13 @@ rctbls(enrichment_obj_wt)
 The `sankey_plot` function generates a three-layer Sankey diagrams connecting metabolites, the metabolite sets (MSets), and the gene sets (GSets) derived from hypeR-GEM. Edge weights between the metabolite and Msets layers reflect the number of shared metabolites, while edges between the MSets and GSets layers reflect the overlap between hypeR-GEM–mapped genes and genes in each GSets. Here we use a toy dataset to illustrate its utility.
 
 ```{r}
-metabolite_signatures <- paste0("m", 1:10)
-
-Msets <- list(Mset1 = c("m1", "m2", "m3"),
-              Mset2 = c("m4","m5", "m6"),
-              Mset3 = c("m7", "m8", "m9", "m10"))
+data("hypeR_object_NECS")
+data("metabolon_msets_list")
+data("gsets_list")
 
+p <- sankey_plot(hypeR_object_NECS, list(metabolon_msets_list$metabolonSupPthwy), list(gsets_list$hallmark), key = "refmet_name",font_size=16,node_width=20)
 
+p
 ```