diff --git a/.gitattributes b/.gitattributes
index 58cf167..a7550d7 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1 +1,2 @@
-/code/MOSuite linguist-vendored
\ No newline at end of file
+/code/MOSuite linguist-vendored
+code/MOSuite linguist-vendored
diff --git a/.github/WORDLIST.txt b/.github/WORDLIST.txt
new file mode 100644
index 0000000..e69de29
diff --git a/.github/workflows/auto-format.yml b/.github/workflows/auto-format.yml
index 5c98340..556cc9e 100644
--- a/.github/workflows/auto-format.yml
+++ b/.github/workflows/auto-format.yml
@@ -3,44 +3,45 @@ name: auto-format
 on:
   workflow_dispatch:
   pull_request:
+    branches: [dev, main]
 
-env:
-  GH_TOKEN: ${{ github.token }}
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 permissions:
   contents: write
   pull-requests: write
 
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
-
 jobs:
   auto-format:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
-        if: github.event_name == 'pull_request'
+      - name: Generate a token
+        id: generate-token
+        uses: actions/create-github-app-token@v2
         with:
-          fetch-depth: 0
-          ref: ${{ github.head_ref }}
-      - uses: actions/checkout@v4
-        if: github.event_name != 'pull_request'
+          app-id: ${{ vars.CCBR_BOT_APP_ID }}
+          private-key: ${{ secrets.CCBR_BOT_PRIVATE_KEY }}
+          owner: ${{ github.repository_owner }}
+
+      - uses: actions/checkout@v7
         with:
-          fetch-depth: 0
-          ref: ${{ github.ref_name }}
+          token: ${{ steps.generate-token.outputs.token }}
+          ref: ${{ github.event_name == 'pull_request' && github.head_ref || github.ref_name }}
 
       - name: git config
         run: |
-          git config --global user.name "github-actions[bot]"
-          git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
-
-      - name: Format R code with air
-        uses: rstudio/shiny-workflows/format-r-code@v1
+          git config --global user.name "CCBR-bot"
+          git config --global user.email "258092125+ccbr-bot@users.noreply.github.com"
 
+      - name: format
+        uses: pre-commit/action@v3.0.1
+        continue-on-error: true
       - name: commit & push
+        if: ${{ github.event_name == 'pull_request' }}
         run: |
           git add .
-          git commit -m "ci: 🤖 auto-format" || echo "nothing to commit"
+          git commit -m "ci: 🤖 auto-format with pre-commit" || echo "nothing to commit"
           git push || echo "nothing to push"
diff --git a/.github/workflows/syncweaver-host-contribute-patch.yml b/.github/workflows/syncweaver-host-contribute-patch.yml
new file mode 100644
index 0000000..e6a2d3d
--- /dev/null
+++ b/.github/workflows/syncweaver-host-contribute-patch.yml
@@ -0,0 +1,190 @@
+name: syncweaver-contribute-patch
+
+on:
+  workflow_dispatch:
+    inputs:
+      source_path:
+        description: Optional tracked source path override; if omitted, source_path is resolved from lockfile.
+        required: false
+        type: string
+      repo_url:
+        description: Optional source repository identifier (URL or OWNER/REPO) used to resolve source_path from lockfile.
+        required: false
+        type: string
+      source_repository:
+        description: Optional source repository in OWNER/REPO format; if omitted, derives from lockfile repo_url.
+        required: false
+        type: string
+      lockfile:
+        description: Path to the syncweaver lockfile.
+        required: false
+        default: .syncweaver-lock.json
+        type: string
+      patch_path:
+        description: Optional patch path override; if omitted, uses source entry patch value from lockfile.
+        required: false
+        type: string
+      source_base_ref:
+        description: Optional source repository base branch for PR; if omitted, uses source entry ref from lockfile.
+        required: false
+        type: string
+
+permissions:
+  contents: read
+
+jobs:
+  resolve-patch-metadata:
+    runs-on: ubuntu-latest
+    outputs:
+      source_path: ${{ steps.resolve.outputs.source_path }}
+      repo_url: ${{ steps.resolve.outputs.repo_url }}
+      source_repository: ${{ steps.resolve.outputs.source_repository }}
+      patch_path: ${{ steps.resolve.outputs.patch_path }}
+      source_base_ref: ${{ steps.resolve.outputs.source_base_ref }}
+      lockfile: ${{ env.LOCKFILE }}
+    env:
+      SOURCE_PATH: ${{ github.event.inputs.source_path || '' }}
+      REPO_URL: ${{ github.event.inputs.repo_url || '' }}
+      SOURCE_REPOSITORY: ${{ github.event.inputs.source_repository || '' }}
+      LOCKFILE: ${{ github.event.inputs.lockfile || '.syncweaver-lock.json' }}
+      PATCH_PATH: ${{ github.event.inputs.patch_path || '' }}
+      SOURCE_BASE_REF: ${{ github.event.inputs.source_base_ref || '' }}
+    steps:
+      - name: Checkout host repository
+        uses: actions/checkout@v6
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.14"
+          cache: pip
+
+      - name: Install syncweaver
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install "git+https://github.com/CCBR/syncweaver.git@main"
+
+      - name: Resolve source and patch metadata
+        id: resolve
+        shell: bash
+        env:
+          SOURCE_PATH_INPUT: ${{ env.SOURCE_PATH }}
+          REPO_URL_INPUT: ${{ env.REPO_URL }}
+          SOURCE_REPOSITORY_INPUT: ${{ env.SOURCE_REPOSITORY }}
+          LOCKFILE_PATH: ${{ env.LOCKFILE }}
+          PATCH_PATH_INPUT: ${{ env.PATCH_PATH }}
+          SOURCE_BASE_REF_INPUT: ${{ env.SOURCE_BASE_REF }}
+          SYNCWEAVER_HOST_CWD: ${{ github.workspace }}
+        run: |
+          python -m syncweaver.contribute_patch
+
+      - name: Print resolved metadata
+        shell: bash
+        run: |
+          set -euo pipefail
+          echo "source_path=${{ steps.resolve.outputs.source_path }}"
+          echo "repo_url=${{ steps.resolve.outputs.repo_url }}"
+          echo "source_repository=${{ steps.resolve.outputs.source_repository }}"
+          echo "patch_path=${{ steps.resolve.outputs.patch_path }}"
+          echo "source_base_ref=${{ steps.resolve.outputs.source_base_ref }}"
+
+  contribute-patch:
+    runs-on: ubuntu-latest
+    needs: resolve-patch-metadata
+    permissions:
+      contents: read
+    env:
+      SOURCE_PATH: ${{ needs.resolve-patch-metadata.outputs.source_path }}
+      REPO_URL: ${{ needs.resolve-patch-metadata.outputs.repo_url }}
+      SOURCE_REPOSITORY: ${{ needs.resolve-patch-metadata.outputs.source_repository }}
+      PATCH_PATH: ${{ needs.resolve-patch-metadata.outputs.patch_path }}
+      SOURCE_BASE_REF: ${{ needs.resolve-patch-metadata.outputs.source_base_ref }}
+      LOCKFILE: ${{ needs.resolve-patch-metadata.outputs.lockfile }}
+    steps:
+      - name: Generate CCBR-bot token
+        id: ccbr_bot
+        uses: actions/create-github-app-token@v1
+        with:
+          app-id: ${{ secrets.CCBR_BOT_APP_ID }}
+          private-key: ${{ secrets.CCBR_BOT_PRIVATE_KEY }}
+
+      - name: Checkout host repository
+        uses: actions/checkout@v6
+        with:
+          path: host
+
+      - name: Checkout source repository
+        uses: actions/checkout@v6
+        with:
+          repository: ${{ env.SOURCE_REPOSITORY }}
+          ref: ${{ env.SOURCE_BASE_REF }}
+          token: ${{ steps.ccbr_bot.outputs.token }}
+          path: source
+
+      - name: Apply patch to source repository
+        id: apply_patch
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          patch_file="$GITHUB_WORKSPACE/host/${PATCH_PATH}"
+          if [[ ! -f "$patch_file" ]]; then
+            echo "Error: patch file not found in host repository: ${PATCH_PATH}" >&2
+            exit 1
+          fi
+
+          branch_stub=$(printf '%s' "$SOURCE_PATH" | tr '/ ' '--' | tr -cd '[:alnum:]._-')
+          if [[ -z "$branch_stub" ]]; then
+            branch_stub="patch"
+          fi
+          branch_name="syncweaver/contribute-patch/${branch_stub}-${GITHUB_RUN_ID}"
+
+          cd "$GITHUB_WORKSPACE/source"
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git switch -c "$branch_name"
+
+          if ! git apply --3way --whitespace=nowarn "$patch_file"; then
+            echo "Error: patch failed to apply cleanly to ${SOURCE_REPOSITORY}@${SOURCE_BASE_REF}" >&2
+            exit 1
+          fi
+
+          if git diff --quiet; then
+            echo "has_changes=false" >> "$GITHUB_OUTPUT"
+          else
+            echo "has_changes=true" >> "$GITHUB_OUTPUT"
+          fi
+          echo "branch_name=$branch_name" >> "$GITHUB_OUTPUT"
+
+      - name: Open pull request in source repository
+        if: steps.apply_patch.outputs.has_changes == 'true'
+        uses: peter-evans/create-pull-request@v7
+        with:
+          token: ${{ steps.ccbr_bot.outputs.token }}
+          path: source
+          base: ${{ env.SOURCE_BASE_REF }}
+          branch: ${{ steps.apply_patch.outputs.branch_name }}
+          delete-branch: true
+          commit-message: "chore(syncweaver): apply host patch for ${{ env.SOURCE_PATH }}"
+          title: "chore(syncweaver): apply host patch for ${{ env.SOURCE_PATH }}"
+          body: |
+            Automated patch contribution from host repository workflow dispatch.
+
+            Inputs used:
+            - source_path: ${{ env.SOURCE_PATH }}
+            - repo_url: ${{ env.REPO_URL }}
+            - source_repository: ${{ env.SOURCE_REPOSITORY }}
+            - source_base_ref: ${{ env.SOURCE_BASE_REF }}
+            - patch_path: ${{ env.PATCH_PATH }}
+            - lockfile: ${{ env.LOCKFILE }}
+
+            Trigger context:
+            - host_repository: ${{ github.repository }}
+            - workflow_run: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
+
+      - name: Print no-op summary
+        if: steps.apply_patch.outputs.has_changes == 'false'
+        shell: bash
+        run: |
+          set -euo pipefail
+          echo "Patch applied cleanly but introduced no source changes. No PR created."
diff --git a/.github/workflows/syncweaver-host-update.yml b/.github/workflows/syncweaver-host-update.yml
new file mode 100644
index 0000000..4e372a3
--- /dev/null
+++ b/.github/workflows/syncweaver-host-update.yml
@@ -0,0 +1,172 @@
+name: syncweaver-host-update
+
+on:
+  repository_dispatch:
+  workflow_dispatch:
+    inputs:
+      source_path:
+        description: Optional tracked source path override for manual runs; if omitted, source_path is resolved from the lockfile.
+        required: false
+        type: string
+      repo_url:
+        description: Optional source repository identifier (URL or OWNER/REPO) used to resolve source_path from lockfile; for repository_dispatch this defaults to client_payload.source_repository.
+        required: false
+        type: string
+      lockfile:
+        description: Path to the syncweaver lockfile.
+        required: false
+        default: .syncweaver-lock.json
+        type: string
+      ref:
+        description: Optional git ref to sync from.
+        required: false
+        type: string
+      remote_subdir:
+        description: Optional remote subdirectory to vendor.
+        required: false
+        type: string
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  resolve-source-paths:
+    runs-on: ubuntu-latest
+    outputs:
+      source_paths: ${{ steps.resolve_source_paths.outputs.source_paths }}
+      source_count: ${{ steps.resolve_source_paths.outputs.source_count }}
+      lockfile: ${{ env.LOCKFILE }}
+      ref: ${{ env.REF }}
+      remote_subdir: ${{ env.REMOTE_SUBDIR }}
+      repo_url: ${{ env.REPO_URL }}
+    env:
+      # workflow_dispatch may provide source_path directly; repository_dispatch usually
+      # omits it so the workflow resolves source_path from lockfile + source_repository.
+      SOURCE_PATH: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.source_path || github.event.client_payload.source_path || '' }}
+      # Prefer explicit repo_url, then fall back to source_repository from dispatch payload.
+      REPO_URL: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.repo_url || github.event.client_payload.repo_url || github.event.client_payload.source_repository || '' }}
+      LOCKFILE: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.lockfile || github.event.client_payload.lockfile || '.syncweaver-lock.json' }}
+      REF: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.ref || github.event.client_payload.ref || '' }}
+      REMOTE_SUBDIR: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.remote_subdir || github.event.client_payload.remote_subdir || '' }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.14"
+          cache: pip
+
+      - name: Install syncweaver
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install "git+https://github.com/CCBR/syncweaver.git@main"
+
+      - name: Resolve source paths
+        id: resolve_source_paths
+        shell: python
+        env:
+          SOURCE_PATH_INPUT: ${{ env.SOURCE_PATH }}
+          REPO_URL_INPUT: ${{ env.REPO_URL }}
+          LOCKFILE_PATH: ${{ env.LOCKFILE }}
+        run: |
+          import json
+          import os
+          import pathlib
+
+          from syncweaver.lockfile import resolve_source_paths_from_lockfile
+
+          source_path_input = os.environ["SOURCE_PATH_INPUT"].strip()
+          repo_url_input = os.environ["REPO_URL_INPUT"].strip()
+          lockfile_path = pathlib.Path(os.environ["LOCKFILE_PATH"])
+          output_path = pathlib.Path(os.environ["GITHUB_OUTPUT"])
+
+          try:
+            resolved_source_paths = resolve_source_paths_from_lockfile(
+              lockfile=lockfile_path,
+              source_path=source_path_input,
+              repo_url=repo_url_input,
+            )
+          except ValueError as exc:
+            raise SystemExit(f"Error: {exc}") from exc
+
+          with output_path.open("a", encoding="utf-8") as fh:
+            fh.write(f"source_paths={json.dumps(resolved_source_paths)}\n")
+            fh.write(f"source_count={len(resolved_source_paths)}\n")
+
+      - name: Print resolved source paths
+        shell: bash
+        run: |
+          set -euo pipefail
+          echo "source_count=${{ steps.resolve_source_paths.outputs.source_count }}"
+          echo "source_paths=${{ steps.resolve_source_paths.outputs.source_paths }}"
+
+  update-source:
+    runs-on: ubuntu-latest
+    needs: resolve-source-paths
+    strategy:
+      fail-fast: false
+      matrix:
+        source_path: ${{ fromJson(needs.resolve-source-paths.outputs.source_paths) }}
+    env:
+      LOCKFILE: ${{ needs.resolve-source-paths.outputs.lockfile }}
+      REF: ${{ needs.resolve-source-paths.outputs.ref }}
+      REMOTE_SUBDIR: ${{ needs.resolve-source-paths.outputs.remote_subdir }}
+      REPO_URL: ${{ needs.resolve-source-paths.outputs.repo_url }}
+    steps:
+      - name: Generate CCBR-bot token
+        id: ccbr_bot
+        uses: actions/create-github-app-token@v1
+        with:
+          app-id: ${{ vars.CCBR_BOT_APP_ID }}
+          private-key: ${{ secrets.CCBR_BOT_PRIVATE_KEY }}
+
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          token: ${{ steps.ccbr_bot.outputs.token }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.14"
+          cache: pip
+
+      - name: Install syncweaver
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install "git+https://github.com/CCBR/syncweaver.git@main"
+
+      - name: Run update-source composite action
+        id: update_source
+        uses: CCBR/syncweaver/actions/update-source@latest
+        with:
+          source_path: ${{ matrix.source_path }}
+          lockfile: ${{ env.LOCKFILE }}
+          ref: ${{ env.REF }}
+          remote_subdir: ${{ env.REMOTE_SUBDIR }}
+
+      - name: Commit changes and open PR
+        uses: peter-evans/create-pull-request@v7
+        with:
+          token: ${{ steps.ccbr_bot.outputs.token }}
+          branch: syncweaver/update-source/${{ matrix.source_path }}
+          delete-branch: true
+          commit-message: "chore(syncweaver): update ${{ matrix.source_path }} from ${{ steps.update_source.outputs.source_repo }}@${{ steps.update_source.outputs.ref }}"
+          title: "chore(syncweaver): update ${{ matrix.source_path }} from ${{ steps.update_source.outputs.source_repo }}@${{ steps.update_source.outputs.ref }}"
+          body: |
+            Automated source update from the update-source workflow.
+
+            Inputs used:
+            - source_path: ${{ matrix.source_path }}
+            - repo_url: ${{ env.REPO_URL }}
+            - lockfile: ${{ env.LOCKFILE }}
+            - ref: ${{ env.REF }}
+            - remote_subdir: ${{ env.REMOTE_SUBDIR }}
+
+            Resolved from lockfile after update:
+            - source_url: ${{ steps.update_source.outputs.source_url }}
+            - ref: ${{ steps.update_source.outputs.ref }}
+            - remote_subdir: ${{ steps.update_source.outputs.remote_subdir }}
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 61d89f6..d3bacfe 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -2,15 +2,19 @@ name: tests
 
 on:
   push:
-    branches: [ main, dev ]
+    branches: [main, dev]
   pull_request:
-    branches: [ main, dev ]
+    branches: [main, dev]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   tests:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
 
       - name: Parse environment.json and set Docker image
         id: docker_image
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..75390d2
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,52 @@
+default_install_hook_types: [pre-commit, commit-msg]
+default_stages: [pre-commit]
+exclude: |
+  (?x)(
+      ^.codeocean/|
+      ^environment/|
+      ^metadata/|
+      ^code/MOSuite|
+      ^code/SCWorkflow|
+      ^code/OMIX*
+   )
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-added-large-files
+        args: ["--maxkb=10240"]
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-json
+  # spell check
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.2
+    hooks:
+      - id: codespell
+        args:
+          [ -I, .github/WORDLIST.txt ]
+  # R formatting
+  - repo: https://github.com/posit-dev/air-pre-commit
+    rev: 0.10.0
+    hooks:
+      - id: air-format
+  - repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.4.3.9028
+    hooks:
+      - id: parsable-R
+  # Python formatting
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.16
+    hooks:
+      - id: ruff-check
+        args: [--fix]
+      - id: ruff-format
+
+  # enforce conventional commit format
+  - repo: https://github.com/compilerla/conventional-pre-commit
+    rev: v4.4.0
+    hooks:
+      - id: conventional-pre-commit
+        stages: [commit-msg]
+        args: []
diff --git a/.syncweaver-lock.json b/.syncweaver-lock.json
new file mode 100644
index 0000000..e770d45
--- /dev/null
+++ b/.syncweaver-lock.json
@@ -0,0 +1,12 @@
+{
+  "host": "NIDAP-Community/MOSuite-diff-counts",
+  "orchestrator": "NIDAP-Community/syncweaver-orchestrator",
+  "syncweaver_version": "0.0.1-dev",
+  "sources": {
+    "code/MOSuite": {
+      "repo_url": "https://github.com/CCBR/MOSuite",
+      "ref": "v0.3.2",
+      "git_sha": "f4465c58a7d04f5feb41d4455a019ca4946a4ca8"
+    }
+  }
+}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 75d9176..fd9185b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,7 @@
 ## Development version
 
 - Improved the Code Ocean parameter UI for the diff counts capsule (#3, @phoman14).
+- Use MOSuite v0.3.2. (#4, @kelly-sovacool)
 
 ## v3.0
 
diff --git a/code/MOSuite/.github/package-versions.txt b/code/MOSuite/.github/package-versions.txt
deleted file mode 100644
index 8d99fc0..0000000
--- a/code/MOSuite/.github/package-versions.txt
+++ /dev/null
@@ -1 +0,0 @@
-any::ggplot2@3.5.2
diff --git a/code/MOSuite/.github/requirements.txt b/code/MOSuite/.github/requirements.txt
new file mode 100644
index 0000000..e69de29
diff --git a/code/MOSuite/.github/workflows/R-CMD-check.yaml b/code/MOSuite/.github/workflows/R-CMD-check.yaml
index 97d3f32..e4a69e6 100644
--- a/code/MOSuite/.github/workflows/R-CMD-check.yaml
+++ b/code/MOSuite/.github/workflows/R-CMD-check.yaml
@@ -32,13 +32,15 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
     steps:
       - uses: actions/checkout@v6
-      - uses: CCBR/actions/install-r-pak@main
+      - uses: r-lib/actions/setup-r@v2
         with:
-          versions-file: .github/package-versions.txt
-          extra-packages: local::.
-          needs: dev
           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: local::.
+          needs: dev
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
@@ -47,10 +49,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v6
-      - uses: CCBR/actions/install-r-pak@main
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: '4.5'
+          use-public-rspm: true
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          r-version: 4.5
-          versions-file: .github/package-versions.txt
           needs: dev
       - name: Lint
         shell: Rscript {0}
diff --git a/code/MOSuite/.github/workflows/auto-format.yml b/code/MOSuite/.github/workflows/auto-format.yml
index bc5d53b..758c5ba 100644
--- a/code/MOSuite/.github/workflows/auto-format.yml
+++ b/code/MOSuite/.github/workflows/auto-format.yml
@@ -38,10 +38,13 @@ jobs:
           git config --global user.name "CCBR-bot"
           git config --global user.email "258092125+ccbr-bot@users.noreply.github.com"
 
-      - uses: CCBR/actions/install-r-pak@main
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: '4.5'
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          r-version: 4.5
-          versions-file: .github/package-versions.txt
           extra-packages: local::.
           needs: dev
 
diff --git a/code/MOSuite/.github/workflows/draft-release.yml b/code/MOSuite/.github/workflows/draft-release.yml
new file mode 100644
index 0000000..3b847ca
--- /dev/null
+++ b/code/MOSuite/.github/workflows/draft-release.yml
@@ -0,0 +1,31 @@
+name: draft-release
+
+on:
+  workflow_dispatch:
+    inputs:
+      version-tag:
+        description: |
+          Semantic version tag for next release.
+          If not provided, it will be determined based on conventional commit history.
+          Example: v2.5.11
+        required: false
+        type: string
+        default: ""
+
+permissions:
+  contents: write
+  pull-requests: write
+  actions: write
+
+jobs:
+  draft-release:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0 # required to include tags
+      - uses: CCBR/actions/draft-release@latest
+        with:
+          github-token: ${{ github.token }}
+          version-tag: ${{ github.event.inputs.version-tag }}
+          ccbr-actions-version: latest
diff --git a/code/MOSuite/.github/workflows/pkgdown.yaml b/code/MOSuite/.github/workflows/pkgdown.yaml
index ac57479..12ff76a 100644
--- a/code/MOSuite/.github/workflows/pkgdown.yaml
+++ b/code/MOSuite/.github/workflows/pkgdown.yaml
@@ -27,10 +27,13 @@ jobs:
     steps:
       - uses: actions/checkout@v6
 
-      - uses: CCBR/actions/install-r-pak@main
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: '4.5'
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          r-version: 4.5
-          versions-file: .github/package-versions.txt
           extra-packages: local::.
           needs: dev
 
diff --git a/code/MOSuite/.github/workflows/post-release.yml b/code/MOSuite/.github/workflows/post-release.yml
new file mode 100644
index 0000000..81ac73f
--- /dev/null
+++ b/code/MOSuite/.github/workflows/post-release.yml
@@ -0,0 +1,24 @@
+name: post-release
+
+on:
+  release:
+    types:
+      - published
+
+permissions:
+  contents: write
+  pull-requests: write
+  actions: write
+
+jobs:
+  cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+      - uses: CCBR/actions/post-release@latest
+        with:
+          github-token: ${{ github.token }}
+          update-sliding-tags: false
+          ccbr-actions-version: latest
diff --git a/code/MOSuite/.github/workflows/test-coverage.yaml b/code/MOSuite/.github/workflows/test-coverage.yaml
index 6531d6f..26f3f0a 100644
--- a/code/MOSuite/.github/workflows/test-coverage.yaml
+++ b/code/MOSuite/.github/workflows/test-coverage.yaml
@@ -35,10 +35,13 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: CCBR/actions/install-r-pak@main
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: '4.5'
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          r-version: 4.5
-          versions-file: .github/package-versions.txt
           needs: dev
 
       - name: Test coverage
diff --git a/code/MOSuite/.pre-commit-config.yaml b/code/MOSuite/.pre-commit-config.yaml
index 7331cb1..a09d9f3 100644
--- a/code/MOSuite/.pre-commit-config.yaml
+++ b/code/MOSuite/.pre-commit-config.yaml
@@ -30,7 +30,7 @@ repos:
     hooks:
       - id: air-format
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9021
+    rev: v0.4.3.9025
     hooks:
       - id: parsable-R
       - id: readme-rmd-rendered
diff --git a/code/MOSuite/CITATION.cff b/code/MOSuite/CITATION.cff
index 541c136..9768535 100644
--- a/code/MOSuite/CITATION.cff
+++ b/code/MOSuite/CITATION.cff
@@ -1,14 +1,14 @@
-# --------------------------------------------
-# CITATION file created with {cffr} R package
+# ------------------------------------------------
+# CITATION.cff file created with {cffr} R package
 # See also: https://docs.ropensci.org/cffr/
-# --------------------------------------------
+# ------------------------------------------------
  
 cff-version: 1.2.0
 message: 'To cite package "MOSuite" in publications use:'
 type: software
 license: MIT
 title: 'MOSuite: R package for differential multi-omics analysis'
-version: 0.3.1
+version: 0.3.2
 doi: 10.5281/zenodo.16371580
 identifiers:
 - description: Archived snapshots of all versions
@@ -71,10 +71,13 @@ references:
   url: https://www.R-project.org/
   authors:
   - name: R Core Team
+    website: https://ror.org/02zz1nj61
   institution:
     name: R Foundation for Statistical Computing
+    website: https://ror.org/05qewa988
     address: Vienna, Austria
   year: '2026'
+  doi: 10.32614/R.manuals
   version: '>= 4.0.0'
 - type: software
   title: assertthat
@@ -215,7 +218,6 @@ references:
     orcid: https://orcid.org/0000-0002-9335-7468
   year: '2026'
   doi: 10.32614/CRAN.package.ggplot2
-  version: < 4.0.0
 - type: software
   title: glue
   abstract: 'glue: Interpreted String Literals'
@@ -278,51 +280,8 @@ references:
   authors:
   - family-names: Smyth
     given-names: Gordon
-  - family-names: Hu
-    given-names: Yifang
-  - family-names: Ritchie
-    given-names: Matthew
-  - family-names: Silver
-    given-names: Jeremy
-  - family-names: Wettenhall
-    given-names: James
-  - family-names: McCarthy
-    given-names: Davis
-  - family-names: Wu
-    given-names: Di
-  - family-names: Shi
-    given-names: Wei
-  - family-names: Phipson
-    given-names: Belinda
-  - family-names: Lun
-    given-names: Aaron
-  - family-names: Thorne
-    given-names: Natalie
-  - family-names: Oshlack
-    given-names: Alicia
-  - family-names: Graaf
-    given-names: Carolyn
-    name-particle: de
-  - family-names: Chen
-    given-names: Yunshun
-  - family-names: Giner
-    given-names: Goknur
-  - family-names: Langaas
-    given-names: Mette
-  - family-names: Ferkingstad
-    given-names: Egil
-  - family-names: Davy
-    given-names: Marcus
-  - family-names: Pepin
-    given-names: Francois
-  - family-names: Choi
-    given-names: Dongseok
-  - family-names: Law
-    given-names: Charity
-  - family-names: Li
-    given-names: Mengbo
-  - family-names: Chen
-    given-names: Lizhong
+    email: smyth@wehi.edu.au
+    orcid: https://orcid.org/0000-0001-9221-2892
   year: '2026'
   doi: 10.18129/B9.bioc.limma
 - type: software
@@ -344,10 +303,13 @@ references:
   notes: Imports
   authors:
   - name: R Core Team
+    website: https://ror.org/02zz1nj61
   institution:
     name: R Foundation for Statistical Computing
+    website: https://ror.org/05qewa988
     address: Vienna, Austria
   year: '2026'
+  doi: 10.32614/R.manuals
 - type: software
   title: options
   abstract: 'options: Simple, Consistent Package Options'
@@ -470,10 +432,13 @@ references:
   notes: Imports
   authors:
   - name: R Core Team
+    website: https://ror.org/02zz1nj61
   institution:
     name: R Foundation for Statistical Computing
+    website: https://ror.org/05qewa988
     address: Vienna, Austria
   year: '2026'
+  doi: 10.32614/R.manuals
 - type: software
   title: stringr
   abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations'
@@ -584,7 +549,7 @@ references:
   doi: 10.32614/CRAN.package.broom
 - type: software
   title: cffr
-  abstract: 'cffr: Generate Citation File Format (''cff'') Metadata for R Packages'
+  abstract: 'cffr: Generate Citation File Format (''CFF'') Metadata for R Packages'
   notes: Suggests
   url: https://docs.ropensci.org/cffr/
   repository: https://CRAN.R-project.org/package=cffr
@@ -961,9 +926,12 @@ references:
   abstract: 'UpSetR: A More Scalable Alternative to Venn and Euler Diagrams for Visualizing
     Intersecting Sets'
   notes: Suggests
-  url: http://github.com/hms-dbmi/UpSetR
+  url: https://github.com/hms-dbmi/UpSetR
   repository: https://CRAN.R-project.org/package=UpSetR
   authors:
+  - family-names: Conway
+    given-names: Jake
+    email: jake.conway@pathai.com
   - family-names: Gehlenborg
     given-names: Nils
     email: nils@hms.harvard.edu
diff --git a/code/MOSuite/DESCRIPTION b/code/MOSuite/DESCRIPTION
index 9f48d10..8f728ed 100644
--- a/code/MOSuite/DESCRIPTION
+++ b/code/MOSuite/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MOSuite
 Title: R package for differential multi-omics analysis
-Version: 0.3.1
+Version: 0.3.2
 Authors@R: c(
     person("Kelly", "Sovacool", , "kelly.sovacool@nih.gov", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3283-829X")),
@@ -29,7 +29,7 @@ Imports:
     DESeq2,
     dplyr,
     edgeR,
-    ggplot2 (< 4.0.0),
+    ggplot2,
     glue,
     htmlwidgets,
     jsonlite,
diff --git a/code/MOSuite/NEWS.md b/code/MOSuite/NEWS.md
index 24d05da..a1c1f01 100644
--- a/code/MOSuite/NEWS.md
+++ b/code/MOSuite/NEWS.md
@@ -1,8 +1,12 @@
+## 0.3.2
+
+- Support ggplot2 v4.0.0 for correlation heatmap plots in `filter_counts()`, `normalize_counts()`, and `batch_correct_counts()`. (#205, @copilot, @kelly-sovacool)
+
 ## MOSuite 0.3.1
 
 - Fix recursion error in `plot_venn_diagram()`. (#188, @kelly-sovacool)
 - Fix S7 dispatch argument mismatch in `plot_read_depth()` and `plot_histogram()`. (#200, @copilot, @kelly-sovacool)
-- Fix crash in `remove_low_count_genes()` when `use_group_based_filtering = TRUE`. (#200, @copilot, @kelly-sovacool)
+- Fix bug in `remove_low_count_genes()` when `use_group_based_filtering = TRUE`. (#200, @copilot, @kelly-sovacool)
 - Fix color palette selection to fall back to random colors with a message when the number of categories exceeds the palette maximum. (#204, @copilot, @kelly-sovacool)
 - Update S7 class, generic, and method documentation to use roxygen2 v8.0.0. (#206, #212, @copilot, @kelly-sovacool)
 - A docker container with only MOSuite's dependencies, not MOSuite itself, is now available: <https://hub.docker.com/r/nciccbr/mosuite-minimal>. (#209, @kelly-sovacool)
diff --git a/code/MOSuite/R/batch-correction.R b/code/MOSuite/R/batch-correction.R
index 7e18183..bcbf63e 100644
--- a/code/MOSuite/R/batch-correction.R
+++ b/code/MOSuite/R/batch-correction.R
@@ -158,6 +158,7 @@ batch_correct_counts <- function(
       group_colname = batch_colname,
       label_colname = label_colname,
       color_values = colors_for_plots,
+      print_plots = FALSE,
       save_plots = FALSE
     ) +
       ggplot2::labs(caption = "batch-corrected counts")
@@ -181,8 +182,7 @@ batch_correct_counts <- function(
       group_colname = batch_colname,
       label_colname = label_colname,
       color_values = colors_for_plots
-    ) +
-      ggplot2::labs(caption = "batch-corrected counts")
+    )
 
     print_or_save_plot(
       pca_plot,
@@ -200,7 +200,8 @@ batch_correct_counts <- function(
       corHM_plot,
       filename = file.path(plots_subdir, "corr_heatmap.png"),
       print_plots = print_plots,
-      save_plots = save_plots
+      save_plots = save_plots,
+      caption = "batch-corrected counts"
     )
   }
 
diff --git a/code/MOSuite/R/filter.R b/code/MOSuite/R/filter.R
index 7e0625f..b520ef1 100644
--- a/code/MOSuite/R/filter.R
+++ b/code/MOSuite/R/filter.R
@@ -216,6 +216,7 @@ filter_counts <- function(
       label_font_size = label_font_size,
       label_offset_y_ = label_offset_y_,
       label_offset_x_ = label_offset_x_,
+      print_plots = FALSE,
       save_plots = FALSE
     ) +
       ggplot2::labs(caption = "filtered counts")
@@ -246,13 +247,13 @@ filter_counts <- function(
         label_colname = label_colname,
         group_colname = group_colname,
         color_values = colors_for_plots
-      ) +
-        ggplot2::labs(caption = "filtered counts")
+      )
       print_or_save_plot(
         corHM,
         filename = file.path(plots_subdir, "corr_heatmap.png"),
         print_plots = print_plots,
-        save_plots = save_plots
+        save_plots = save_plots,
+        caption = "filtered counts"
       )
     }
 
diff --git a/code/MOSuite/R/normalize.R b/code/MOSuite/R/normalize.R
index e6ebd76..4823217 100644
--- a/code/MOSuite/R/normalize.R
+++ b/code/MOSuite/R/normalize.R
@@ -129,6 +129,7 @@ normalize_counts <- function(
       label_font_size = label_font_size,
       label_offset_y_ = label_offset_y_,
       label_offset_x_ = label_offset_x_,
+      print_plots = FALSE,
       save_plots = FALSE
     ) +
       ggplot2::labs(caption = "normalized counts")
@@ -156,13 +157,13 @@ normalize_counts <- function(
         group_colname = group_colname,
         label_colname = label_colname,
         color_values = colors_for_plots
-      ) +
-        ggplot2::labs(caption = "normalized counts")
+      )
       print_or_save_plot(
         corHM_plot,
         filename = file.path(plots_subdir, "corr_heatmap.png"),
         print_plots = print_plots,
-        save_plots = save_plots
+        save_plots = save_plots,
+        caption = "normalized counts"
       )
     }
 
diff --git a/code/MOSuite/R/plots.R b/code/MOSuite/R/plots.R
index c814b78..1d5770e 100644
--- a/code/MOSuite/R/plots.R
+++ b/code/MOSuite/R/plots.R
@@ -3,12 +3,15 @@
 #' If `save_plots` is `TRUE`, the plot will be saved as an image to the path at
 #' `file.path(plots_dir, filename)`.
 #' If `plot_obj` is a ggplot, `ggplot2::ggsave()` is used to save the image.
-#' Otherwise, `graphics_device` is used (`grDevice::png()` by default).
+#' Otherwise, `graphics_device` is used (`grDevices::png()` by default).
 #'
 #' @inheritParams option_params
 #' @param plot_obj plot object (e.g. ggplot, ComplexHeatmap...)
 #' @param filename name of the output file. will be joined with the `plots_dir` option.
-#' @param graphics_device Default: `grDevice::png()`. Only used if the plot is not a ggplot.
+#' @param graphics_device Default: `grDevices::png()`. Only used if the plot is not a ggplot.
+#' @param caption optional caption text to add to the plot. For ggplot objects, this is
+#'   added via `ggplot2::labs(caption = caption)`. For `ComplexHeatmap` objects, the
+#'   caption is rendered at the bottom of the graphics device using `grid::grid.text()`.
 #' @param ... arguments forwarded to `ggplot2::ggsave()`
 #'
 #' @return invisibly returns the path where the plot image was saved to the disk
@@ -22,10 +25,30 @@ print_or_save_plot <- function(
   save_plots = options::opt("save_plots"),
   plots_dir = options::opt("plots_dir"),
   graphics_device = grDevices::png,
+  caption = NULL,
   ...
 ) {
+  draw_heatmap_with_caption <- function(hm) {
+    ComplexHeatmap::draw(hm)
+    if (!is.null(caption)) {
+      grid::grid.text(
+        caption,
+        x = grid::unit(0.5, "npc"),
+        y = grid::unit(2, "mm"),
+        just = "bottom",
+        gp = grid::gpar(fontsize = 9, col = "grey40")
+      )
+    }
+  }
+  if (!is.null(caption) && inherits(plot_obj, "ggplot")) {
+    plot_obj <- plot_obj + ggplot2::labs(caption = caption)
+  }
   if (isTRUE(print_plots)) {
-    print(plot_obj)
+    if (inherits(plot_obj, c("Heatmap", "HeatmapList"))) {
+      draw_heatmap_with_caption(plot_obj)
+    } else {
+      print(plot_obj)
+    }
   }
   if (isTRUE(save_plots)) {
     # create output directory if it doesn't exist
@@ -42,10 +65,14 @@ print_or_save_plot <- function(
       ggplot2::ggsave(filename = filename, plot = plot_obj, ...)
     } else if (inherits(plot_obj, "htmlwidget")) {
       htmlwidgets::saveWidget(plot_obj, filename, ...)
+    } else if (inherits(plot_obj, c("Heatmap", "HeatmapList"))) {
+      graphics_device(file = filename)
+      on.exit(grDevices::dev.off(), add = TRUE)
+      draw_heatmap_with_caption(plot_obj)
     } else {
       graphics_device(file = filename)
+      on.exit(grDevices::dev.off(), add = TRUE)
       plot(plot_obj)
-      grDevices::dev.off()
     }
   }
   return(invisible(filename))
diff --git a/code/MOSuite/codemeta.json b/code/MOSuite/codemeta.json
index cb4a191..5cf8660 100644
--- a/code/MOSuite/codemeta.json
+++ b/code/MOSuite/codemeta.json
@@ -32,5 +32,5 @@
   "license": "https://spdx.org/licenses/MIT",
   "name": "MOSuite: R package for differential multi-omics analysis",
   "url": "https://ccbr.github.io/MOSuite/",
-  "version": "0.3.1"
+  "version": "0.3.1.9001"
 }
diff --git a/code/MOSuite/docker/Dockerfile b/code/MOSuite/docker/Dockerfile
index a97d70b..73385eb 100644
--- a/code/MOSuite/docker/Dockerfile
+++ b/code/MOSuite/docker/Dockerfile
@@ -21,8 +21,8 @@ RUN mamba install -y -c conda-forge \
     r-colorspace \
     r-dendextend \
     r-devtools \
+    r-ggplot2 \
     r-dplyr \
-    "r-ggplot2 <4.0.0" \
     r-ggrepel \
     r-gridExtra \
     r-here \
diff --git a/code/MOSuite/docker/Dockerfile_minimal b/code/MOSuite/docker/Dockerfile_minimal
index eb91b2c..014755d 100644
--- a/code/MOSuite/docker/Dockerfile_minimal
+++ b/code/MOSuite/docker/Dockerfile_minimal
@@ -21,8 +21,8 @@ RUN mamba install -y -c conda-forge \
     r-colorspace \
     r-dendextend \
     r-devtools \
+    r-ggplot2 \
     r-dplyr \
-    "r-ggplot2 <4.0.0" \
     r-ggrepel \
     r-gridExtra \
     r-here \
diff --git a/code/MOSuite/inst/extdata/galaxy/galaxy.R b/code/MOSuite/inst/extdata/galaxy/galaxy.R
index 3d92b9f..33df8ce 100644
--- a/code/MOSuite/inst/extdata/galaxy/galaxy.R
+++ b/code/MOSuite/inst/extdata/galaxy/galaxy.R
@@ -135,9 +135,7 @@ update_function_template <- function(
       arg_name <- template[[arg_type]][[i]]$key
       if (arg_name %in% names(func_meta$args)) {
         arg_meta <- template[[arg_type]][[i]]
-        arg_meta$description <- safe_rd_to_md(
-          func_meta$args[[arg_name]]$description
-        )
+        arg_meta$description <- safe_rd_to_md(func_meta$args[[arg_name]]$description)
         arg_meta$defaultValue <- func_meta$args[[arg_name]]$defaultValue
         args_in_template <- c(args_in_template, arg_name)
         new_template[[arg_type]][[
diff --git a/code/MOSuite/man/print_or_save_plot.Rd b/code/MOSuite/man/print_or_save_plot.Rd
index 4d22ef1..450ea1d 100644
--- a/code/MOSuite/man/print_or_save_plot.Rd
+++ b/code/MOSuite/man/print_or_save_plot.Rd
@@ -11,6 +11,7 @@ print_or_save_plot(
   save_plots = options::opt("save_plots"),
   plots_dir = options::opt("plots_dir"),
   graphics_device = grDevices::png,
+  caption = NULL,
   ...
 )
 }
@@ -25,7 +26,11 @@ print_or_save_plot(
 
 \item{plots_dir}{Path where plots are saved when \code{moo_save_plots} is \code{TRUE} (Defaults to \code{"figures/"}, overwritable using option 'moo_plots_dir' or environment variable 'MOO_PLOTS_DIR')}
 
-\item{graphics_device}{Default: \code{grDevice::png()}. Only used if the plot is not a ggplot.}
+\item{graphics_device}{Default: \code{grDevices::png()}. Only used if the plot is not a ggplot.}
+
+\item{caption}{optional caption text to add to the plot. For ggplot objects, this is
+added via \code{ggplot2::labs(caption = caption)}. For \code{ComplexHeatmap} objects, the
+caption is rendered at the bottom of the graphics device using \code{grid::grid.text()}.}
 
 \item{...}{arguments forwarded to \code{ggplot2::ggsave()}}
 }
@@ -36,7 +41,7 @@ invisibly returns the path where the plot image was saved to the disk
 If \code{save_plots} is \code{TRUE}, the plot will be saved as an image to the path at
 \code{file.path(plots_dir, filename)}.
 If \code{plot_obj} is a ggplot, \code{ggplot2::ggsave()} is used to save the image.
-Otherwise, \code{graphics_device} is used (\code{grDevice::png()} by default).
+Otherwise, \code{graphics_device} is used (\code{grDevices::png()} by default).
 }
 \seealso{
 Other plotters:
diff --git a/code/MOSuite/tests/testthat/test-plot_volcano_enhanced.R b/code/MOSuite/tests/testthat/test-plot_volcano_enhanced.R
index 6f351ca..a115797 100644
--- a/code/MOSuite/tests/testthat/test-plot_volcano_enhanced.R
+++ b/code/MOSuite/tests/testthat/test-plot_volcano_enhanced.R
@@ -1,4 +1,5 @@
 test_that("plot_volcano_enhanced works on nidap dataset", {
+  skip_on_ci()
   expect_snapshot(
     df_volc_enh <- plot_volcano_enhanced(
       nidap_deg_analysis,
diff --git a/code/MOSuite/tests/testthat/test-plots.R b/code/MOSuite/tests/testthat/test-plots.R
index 43ada4f..bb965f3 100644
--- a/code/MOSuite/tests/testthat/test-plots.R
+++ b/code/MOSuite/tests/testthat/test-plots.R
@@ -1,6 +1,7 @@
 set.seed(20250225)
-test_that("save_or_print_plot works for ComplexHeatmap", {
-  p <- plot_corr_heatmap(
+
+corr_heatmap_fixture <- function() {
+  plot_corr_heatmap(
     nidap_filtered_counts |>
       as.data.frame(),
     sample_metadata = as.data.frame(nidap_sample_metadata),
@@ -23,7 +24,59 @@ test_that("save_or_print_plot works for ComplexHeatmap", {
       "#878500"
     )
   )
-  skip()
+}
+
+test_that("print_or_save_plot saves ComplexHeatmap to disk without error", {
+  p <- corr_heatmap_fixture()
+  outfile <- tempfile(fileext = ".png")
+  result <- print_or_save_plot(
+    p,
+    filename = outfile,
+    print_plots = FALSE,
+    save_plots = TRUE,
+    plots_dir = "",
+    caption = "filtered counts"
+  )
+  expect_equal(result, outfile)
+  expect_true(file.exists(outfile))
+  expect_gt(file.size(outfile), 0)
+})
+
+test_that("print_or_save_plot saves ggplot without error", {
+  p <- plot_read_depth(nidap_clean_raw_counts)
+  outfile <- tempfile(fileext = ".png")
+  result <- print_or_save_plot(
+    p,
+    filename = outfile,
+    print_plots = FALSE,
+    save_plots = TRUE,
+    plots_dir = "",
+    caption = "normalized counts"
+  )
+  expect_equal(result, outfile)
+  expect_true(file.exists(outfile))
+  expect_gt(file.size(outfile), 0)
+})
+
+test_that("print_or_save_plot prints ComplexHeatmap with caption without error", {
+  p <- corr_heatmap_fixture()
+  outfile <- tempfile(fileext = ".png")
+  withr::with_png(outfile, {
+    result <- print_or_save_plot(
+      p,
+      filename = outfile,
+      print_plots = TRUE,
+      save_plots = FALSE,
+      plots_dir = "",
+      caption = "batch-corrected counts"
+    )
+  })
+  expect_equal(result, outfile)
+})
+
+test_that("save_or_print_plot works for ComplexHeatmap", {
+  p <- corr_heatmap_fixture()
+  skip_on_ci()
   expect_snapshot_file(
     print_or_save_plot(
       p,
@@ -37,7 +90,7 @@ test_that("save_or_print_plot works for ComplexHeatmap", {
 })
 test_that("save_or_print_plot works for ggplot", {
   p <- plot_read_depth(nidap_clean_raw_counts)
-  skip()
+  skip_on_ci()
   expect_snapshot_file(
     print_or_save_plot(
       p,