speedup enrichment() via Rcpp

Author: zhizuio

.gitignore

@@ -2,7 +2,10 @@
 .Rbuildignore
 .vscode
 
+README.html
+cleanup
 test.R
+test_build*.R
 sankey.html
 .RData
 .tar.gz

DESCRIPTION

@@ -1,24 +1,19 @@
 Package: EnrichIntersect
 Type: Package
 Title: Enrichment Analysis and Intersecting Sankey Diagram
-Version: 0.7
-Date: 2024-03-14
+Version: 1.0
 URL: https://github.com/ocbe-uio/EnrichIntersect
 BugReports: https://github.com/ocbe-uio/EnrichIntersect/issues
 Authors@R: c(person("Zhi", "Zhao", email = "zhi.zhao@medisin.uio.no", role = c("aut","cre")), person("Manuela", "Zucknick", email = "manuela.zucknick@medisin.uio.no", role = c("aut")), person("Tero", "Aittokallio", email = "t.a.aittokallio@medisin.uio.no", role = c("ctb")))
 Description: A flexible tool for enrichment analysis based on user-defined sets. It allows users to perform over-representation analysis of the custom sets among any specified ranked feature list, hence making enrichment analysis applicable to various types of data from different scientific fields. 'EnrichIntersect' also enables an interactive means to visualize identified associations based on, for example, the mix-lasso model (Zhao et al., 2022 <doi:10.1016/j.isci.2022.104767>) or similar methods.
 License: MIT + file LICENSE
 Depends: R (>= 4.0)
 Encoding: UTF-8
-RoxygenNote: 7.2.3
-Imports: ggplot2, dplyr, networkD3, jsonlite, htmlwidgets, webshot2,
+LinkingTo: Rcpp, RcppArmadillo
+Imports: Rcpp, ggplot2, dplyr, networkD3, jsonlite, htmlwidgets, webshot2,
         stats, methods, grDevices
 Suggests: knitr
 LazyData: true
 VignetteBuilder: knitr
-NeedsCompilation: no
-Packaged: 2024-03-14 15:42:21 UTC; zhiz
-Author: Zhi Zhao [aut, cre],
-  Manuela Zucknick [aut],
-  Tero Aittokallio [ctb]
-Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
+NeedsCompilation: yes
+Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -3,6 +3,7 @@
 export(enrichment)
 export(intersectSankey)
 import(ggplot2)
+importFrom(Rcpp,sourceCpp)
 importFrom(dplyr,"%>%")
 importFrom(grDevices,hcl.colors)
 importFrom(htmlwidgets,onRender)
@@ -12,6 +13,5 @@ importFrom(methods,hasArg)
 importFrom(networkD3,JS)
 importFrom(networkD3,sankeyNetwork)
 importFrom(stats,p.adjust)
-importFrom(utils,setTxtProgressBar)
-importFrom(utils,txtProgressBar)
 importFrom(webshot2,webshot)
+useDynLib(EnrichIntersect, .registration = TRUE)

NEWS.md

@@ -1,3 +1,7 @@
+# EnrichIntersect 1.0
+
+- Added Rcpp code to speedup function `enrichment()`
+
 # EnrichIntersect 0.7
 
 - Fixed issue with the legend of p<0.05

R/EnrichIntersect-package.R

@@ -0,0 +1,12 @@
+#' @keywords internal
+#' @aliases EnrichIntersect-package NULL
+#'
+#'
+"_PACKAGE"
+
+## usethis namespace: start
+#' @useDynLib EnrichIntersect, .registration = TRUE
+#' @importFrom Rcpp sourceCpp
+## usethis namespace: end
+NULL
+

R/RcppExports.R

@@ -0,0 +1,7 @@
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+enrichment_core_original <- function(x, set_indices, alpha = 0.0, normalize = TRUE, permute_n = 100L) {
+    .Call(`_EnrichIntersect_enrichment_core_original`, x, set_indices, alpha, normalize, permute_n)
+}
+