add degpattern actions

Author: lpantano

.github/workflows/run_degpattern.yml

@@ -0,0 +1,71 @@
+name: DEG Pattern Report
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - '04_gene_patterns/DEGpattern.qmd'
+  pull_request:
+    branches: [main]
+    paths:
+      - '04_gene_patterns/DEGpattern.qmd'
+  workflow_dispatch:
+
+jobs:
+  r-degpattern:
+    runs-on: ubuntu-22.04
+
+    env:
+      RENV_PATHS_ROOT: ~/.local/share/renv  # persistent cache location
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Install system dependencies for R packages
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y build-essential libcurl4-openssl-dev libssl-dev libxml2-dev libgit2-dev libmagick++-dev libharfbuzz-dev libfribidi-dev
+        shell: bash
+
+      - name: Cache R packages (renv)
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.RENV_PATHS_ROOT }}
+          key: ${{ runner.os }}-renv-${{ hashFiles('04_gene_patterns/renv.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-renv-
+
+      - name: Set repositories
+        run: Rscript ubuntu.R
+
+      - name: Restore environment from renv.lock
+        run: |
+          install.packages("renv", repos = "https://cloud.r-project.org")
+          renv::restore(prompt = FALSE, lockfile = "04_gene_patterns/renv.lock")
+        shell: Rscript {0}
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Run DEGpattern report
+        id: render_degpattern
+        run: |
+          cd 04_gene_patterns
+          quarto render DEGpattern.qmd
+        shell: bash
+
+      - name: Deploy HTML to gh-pages
+        if: success()
+        run: |
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+          git fetch origin gh-pages || git checkout --orphan gh-pages
+          git switch gh-pages || git checkout -b gh-pages
+          git add 04_gene_patterns/DEGpattern.html
+          git commit -m "Deploy DEGpattern.html [skip ci]" || echo "No changes to commit"
+          git push origin gh-pages
+        shell: bash

04_gene_patterns/DEGpattern.qmd

@@ -60,6 +60,8 @@ library(ggplot2)
 library(knitr)
 library(glue)
 library(R.utils)
+library(grafify)
+library(ggprism)
 ggplot2::theme_set(ggprism::theme_prism(base_size = 12))
 catCols <- as.vector(grafify:::graf_palettes[["kelly"]])
 scale_colour_discrete <- function(...) {

04_gene_patterns/WGCNA.qmd

@@ -82,14 +82,17 @@ library(flashClust)
 library(gridExtra)
 library(DT)
 library(AnnotationDbi)
-library(bcbioR)
-
 library(knitr)
 library(ggprism)
+library()
+library(grafify)
+library(ggprism)
+ggplot2::theme_set(ggprism::theme_prism(base_size = 12))
+catCols <- as.vector(grafify:::graf_palettes[["kelly"]])
+scale_colour_discrete <- function(...) {
+  scale_colour_manual(..., values = catCols)
+}
 
-
-colors <- cb_friendly_cols(1:15)
-ggplot2::theme_set(theme_prism(base_size = 14))
 opts_chunk[["set"]](
   cache = F,
   cache.lazy = FALSE,