website updates

.Rbuildignore

@@ -2,7 +2,6 @@ datasets
 scripts
 LICENSE\.md
 compile_flags.txt
-^man/figures
 .RData$
 ^vignettes/pbmc_cache
 ^vignettes/pbmc_files
@@ -13,4 +12,5 @@ compile_flags.txt
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
-^index\.md$
+^index\.md$
+^\.github$

.github/.gitignore

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

.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@v4
+
+      - 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

DESCRIPTION

@@ -41,3 +41,5 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 License: GPL (>= 3)
 Config/testthat/edition: 3
+URL: https://scmethods.github.io/scregclust/, https://github.com/scmethods/scregclust/ 
+BugReports: https://github.com/scmethods/scregclust/issues

README.md

@@ -8,14 +8,14 @@
 
 The goal of *scregclust* is to cluster genes by regulatory programs. To do so, clusters are associated with regulatory programs and target genes are allocated to clusters with best fitting regulatory programs.
 
--   The documentation for this package can be found at [https://sven-nelander.github.io/scregclust](https://sven-nelander.github.io/scregclust)
+-   The documentation for this package can be found at [https://scmethods.github.io/scregclust](https://scmethods.github.io/scregclust)
 -   A detailed description of the algorithm and an in-depth evaluation of its properties can be found in our [pre-print on bioRxiv](https://doi.org/10.1101/2023.03.10.532041 "Reconstructing the regulatory programs underlying the phenotypic plasticity of neural cancers"){.uri}.
 
 ## Installation
 
-You can install the development version of *scregclust* from [GitHub](https://github.com/sven-nelander/scregclust) with:
+You can install the development version of *scregclust* from [GitHub](https://github.com/scmethods/scregclust) with:
 
 ```r
 # install.packages("devtools")
-devtools::install_github("sven-nelander/scregclust")
+devtools::install_github("scmethods/scregclust")
 ```

_pkgdown.yml

@@ -1,31 +1,38 @@
-url: ~
+url: https://scmethods.github.io/scregclust/
 template:
   bootstrap: 5
+navbar:
+  structure:
+  components:
+    articles:
+      text: Vignettes
+      menu:
+      - text: Demonstration of workflow
+        href: articles/pbmc.html
 reference:
-- title: "Setting up and performing clustering"
-  desc: >
-    Functions to prepare the input data and to perform single-cell
-    regulatory-driven clustering.
+- title: Setting up and performing clustering
+  desc: |
+    Functions to prepare the input data and to perform single-cell regulatory-driven clustering.
   contents:
   - scregclust_format
   - scregclust
-- title: "Plotting and evaluation"
-  desc: >
+- title: Plotting and evaluation
+  desc: |
     Functions which help in plotting and evaluating results.
   contents:
   - plot_cluster_count_helper
   - plot_regulator_network
   - plot_silhouettes
-- title: "Utility functions"
-  desc: >
+- title: Utility functions
+  desc: |
     Functions that make accessing aspects of the results easier.
   contents:
   - get_target_clusters
   - get_regulator_list
   - get_rand_indices
   - get_num_final_configs
   - get_avg_num_regulators
-- title: "Other helpers"
+- title: Other helpers
   contents:
   - available_results
   - cluster_overlap

index.md

@@ -4,8 +4,10 @@
 
 <!-- badges: end -->
 
-![A diagram illustrating the *scregclust* algorithm.](man/figures/overview_fig1A_bg.png "Illustration of the scregclust algorithm")
+![](overview_fig1A_bg.png)
 
-The goal of *scregclust* is to cluster genes by regulatory programs. To do so, clusters are associated with regulatory programs and target genes are allocated to clusters with best fitting regulatory programs.
+## Introduction
+
+The goal of *scregclust* is to cluster genes by regulatory programs. To do so, clusters are associated with regulators and target genes are allocated to clusters with best fitting regulatory programs.
 
 A detailed description of the algorithm and an in-depth evaluation of its properties can be found in our pre-print on bioRxiv: [DOI 10.1101/2023.03.10.532041](https://doi.org/10.1101/2023.03.10.532041 "Reconstructing the regulatory programs underlying the phenotypic plasticity of neural cancers")