chore(syncweaver): update tracked sources from CCBR/MOSuite@v0.3.2

.syncweaver-lock.json

@@ -4,8 +4,8 @@
   "sources": {
     "code/MOSuite": {
       "repo_url": "https://github.com/CCBR/MOSuite",
-      "ref": "main",
-      "git_sha": "c09ee39f9b282237f13d88dcf4cdfed965209c68",
+      "ref": "v0.3.2",
+      "git_sha": "f4465c58a7d04f5feb41d4455a019ca4946a4ca8",
       "installed_by": [
         "syncweaver"
       ]

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}

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
 

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

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
 

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

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

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

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,

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)

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"
     )
   }
 

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"
       )
     }