Merge branch 'master' into master

.Rbuildignore

@@ -0,0 +1,11 @@
+^src/\.cargo$
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.github$
+^\.lintr$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^logo\.svg$
+^build_hash\.py$
+^\.cargo$

.cargo/config.toml

@@ -0,0 +1,2 @@
+[net]
+git-fetch-with-cli = true

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/ISSUE_TEMPLATE/bug-report.md

@@ -0,0 +1,10 @@
+---
+name: Bug Report
+about: Bug/crash in R package
+title: ''
+labels: bug
+assignees: iblacksand
+
+---
+
+Description of bug and steps to reproduce.

.github/ISSUE_TEMPLATE/installation-issue.md

@@ -0,0 +1,11 @@
+---
+name: Installation Issue
+about: Issue with installing the R package
+title: ''
+labels: Installation
+assignees: iblacksand
+
+---
+
+Platform (macOS, Windows, Linux, etc): PLATFORM
+Description of issue:

.github/ISSUE_TEMPLATE/question.md

@@ -0,0 +1,10 @@
+---
+name: Question
+about: Question about the R package that is not a bug.
+title: ''
+labels: question
+assignees: iblacksand
+
+---
+
+

.github/ISSUE_TEMPLATE/r-vs--rust-difference.md

@@ -0,0 +1,12 @@
+---
+name: R vs. Rust Difference
+about: Results differ between R and Rust Version
+title: ''
+labels: bug, Version Difference
+assignees: iblacksand
+
+---
+
+<!--- Your results may differ because of the data update, not because of the R package itself. You can verify that it is not because of the data update by following the instructions here: <LINK>. If you are unsure how to follow those instructions, or couldn't verify, please feel free to submit an issue here.--->
+
+Description of the result that you previously got in the original version, and the new result that you got.

.github/workflows/check-standard.yaml

@@ -0,0 +1,58 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: macos-latest, r: "release" }
+          - { os: windows-latest, r: "release" }
+          - { os: ubuntu-latest, r: "devel", http-user-agent: "release" }
+          - { os: ubuntu-latest, r: "release" }
+          - { os: ubuntu-latest, r: "oldrel-1" }
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - name: Install stable toolchain
+        if: ${{startsWith(matrix.config.os, 'windows')}}
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          target: x86_64-pc-windows-msvc
+          profile: minimal
+          default: true
+
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/windows-compile.yml

@@ -0,0 +1,68 @@
+on:
+  push:
+    tags:
+      - "windows*"
+
+name: Build Windows
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        target:
+          - x86_64
+          - i686
+
+    name: build-${{ matrix.target }}-pc-windows-msvc
+
+    runs-on: windows-latest
+
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v2
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: "release"
+          use-public-rspm: true
+          rtools-version: "42"
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          target: ${{ matrix.target }}-pc-windows-msvc
+          profile: minimal
+          default: true
+
+      - name: Run cargo build
+        uses: actions-rs/cargo@v1
+        with:
+          command: build
+          args: --release --target=${{ matrix.target }}-pc-windows-msvc --manifest-path=src/rust/Cargo.toml
+
+      - name: List files
+        run: ls ./src/rust/target/${{ matrix.target }}-pc-windows-msvc/release/
+        shell: bash
+
+      - name: Create Release
+        id: create_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ github.ref }}-${{ matrix.target }}
+          release_name: Release ${{ github.ref }}-${{ matrix.target }}
+          draft: false
+          prerelease: true
+      - name: Upload Release Asset
+        id: upload-release-asset
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }}
+          asset_path: ./src/rust/target/${{ matrix.target }}-pc-windows-msvc/release/WebGestaltR.lib
+          asset_name: WebGestaltR.lib
+          asset_content_type: application/octet-stream

.gitignore

@@ -2,4 +2,46 @@
 .Rproj.user
 .DS_Store
 .Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
 .vscode
+.DS_Store
+_site
+index.md
+docs
+inst/doc

.lintr

@@ -0,0 +1,7 @@
+linters: linters_with_defaults(
+    line_length_linter = NULL, 
+    commented_code_linter = NULL,
+    no_tab_linter = NULL,
+    object_name_linter = NULL
+  )
+

DESCRIPTION

@@ -5,20 +5,29 @@ Version: 0.4.6
 Date: 2023-05-31
 Authors@R: c(
         person("Jing", "Wang", email = "[email protected]", role = "aut"),
-        person("Yuxing", "Liao", email = "[email protected]", role = c("aut", "cre")),
+        person("John", "Elizarraras", email = "[email protected]", role = c("aut", "cre")),
+        person("Yuxing", "Liao", email = "[email protected]", role = c("aut")),
         person("Eric", "Jaehnig", email = "[email protected]", role = c("ctb")),
         person("Zhiao", "Shi", email = "[email protected]", role = c("ctb")),
         person("Quanhu", "Sheng", email = "[email protected]", role = c("ctb"))
         )
 Description: The web version WebGestalt <https://www.webgestalt.org> supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.
 License: LGPL
-URL: https://github.com/bzhanglab/WebGestaltR
+URL: https://github.com/bzhanglab/WebGestaltR,
+    https://iblacksand.github.io/WebGestaltR/
 LazyLoad: yes
-Depends: R (>= 3.3)
+Depends: R (>= 4.0)
 Imports: methods, dplyr, doRNG, readr, parallel (>= 3.3.2),
         doParallel (>= 1.0.10), foreach (>= 1.4.0),
         jsonlite, httr, rlang, svglite,
-        igraph, whisker, apcluster, Rcpp
+        igraph, whisker, apcluster, Rcpp, cluster, rextendr
 NeedsCompilation: yes
 LinkingTo: Rcpp
 RoxygenNote: 7.2.3
+SystemRequirements: Cargo (Rust's package manager), rustc v1.63.0+
+Config/rextendr/version: 0.3.1
+Encoding: UTF-8
+Suggests: 
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr

NAMESPACE

@@ -4,6 +4,7 @@ export(GOSlimSummary)
 export(IDMapping)
 export(WebGestaltR)
 export(WebGestaltRBatch)
+export(WebGestaltRMultiOmics)
 export(WebGestaltR_batch)
 export(affinityPropagation)
 export(formatCheck)
@@ -29,6 +30,7 @@ import(methods)
 import(utils)
 importFrom(Rcpp,sourceCpp)
 importFrom(apcluster,apcluster)
+importFrom(cluster,pam)
 importFrom(doParallel,registerDoParallel)
 importFrom(doRNG,"%dorng%")
 importFrom(dplyr,"%>%")
@@ -37,6 +39,7 @@ importFrom(dplyr,bind_rows)
 importFrom(dplyr,desc)
 importFrom(dplyr,distinct)
 importFrom(dplyr,filter)
+importFrom(dplyr,group_by)
 importFrom(dplyr,inner_join)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
@@ -73,3 +76,4 @@ importFrom(tools,file_ext)
 importFrom(whisker,rowSplit)
 importFrom(whisker,whisker.render)
 useDynLib(WebGestaltR)
+useDynLib(WebGestaltR, .registration = TRUE)