Merge branch 'dev' into circos_factorization

.github/copy_to_branch.sh

@@ -0,0 +1,30 @@
+# Designate desired directories and files
+SRC_FOLDER_PATHS=(data-raw man R tests vignettes)
+SRC_FILE_PATHS=(DESCRIPTION LICENSE NAMESPACE NEWS.md README.md inst/CITATION)
+
+# Get files from directories
+FILES=$(find "${SRC_FOLDER_PATHS[@]}" -type f)
+
+# Add indicated individual files
+for F in "${SRC_FILE_PATHS[@]}"
+do
+FILES+=" ${F}"
+done
+
+echo "${FILES[@]}"
+
+# Pass these to github:
+git config --global user.name 'GitHub Action'
+git config --global user.email '[email protected]'
+# Fetch branches
+git fetch
+# Checkout target branch                         
+git checkout $TARGET_BRANCH
+# copy files from the branch the action is being run upon
+SRC_BRANCH=$(git symbolic-ref --short HEAD)
+git checkout $SRC_BRANCH -- $FILES
+# Commit to the repository (ignore if no changes)
+git add -A
+git diff-index --quiet HEAD ||  git commit -am "update files"
+# Push to remote branch
+git push origin $TARGET_BRANCH 

.github/workflows/bioc_branch.yml

@@ -0,0 +1,22 @@
+name: Update Bioconductor package files
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  copy:
+    name: Copy files
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: copy
+        env:
+          TARGET_BRANCH: 'master'
+        run: .github/copy_to_branch.sh
+        shell: bash

.github/workflows/document.yaml

@@ -0,0 +1,43 @@
+# 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:
+      paths: ["R/**"]
+    workflow_dispatch:
+
+name: documentation-update
+
+jobs:
+    document:
+      runs-on: ubuntu-latest
+      env:
+        GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      steps:
+        - name: Checkout repo
+          uses: actions/checkout@v3
+          with:
+            fetch-depth: 0
+
+        - name: Setup R
+          uses: r-lib/actions/setup-r@v2
+          with:
+            use-public-rspm: true
+
+        - name: Install dependencies
+          uses: r-lib/actions/setup-r-dependencies@v2
+          with:
+            extra-packages: any::roxygen2
+            needs: roxygen2
+
+        - name: Document
+          run: roxygen2::roxygenise()
+          shell: Rscript {0}
+
+        - name: Commit and push changes
+          run: |
+            git config --local user.name "$GITHUB_ACTOR"
+            git config --local user.email "[email protected]"
+            git add man/\* NAMESPACE DESCRIPTION
+            git commit -m "Update documentation" || echo "No changes to commit"
+            git pull --ff-only
+            git push origin

.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-update
+
+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
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = TRUE)
+        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/pull_request_template.md

@@ -0,0 +1,18 @@
+This is a code review template, it will be displayed after each pull request. 
+We do code reviews because we care about quality of our codebase and because we care about long-term development goals.
+We do not do code reviews to blame the ones who contribute. There is no seniority in this process and there is no perfect code, 
+we just want to avoid storing code that is not OK.
+
+## For the submitter
+
+- [ ] `R CMD build` & `R CMD check` pass
+- [ ] `BiocCheck` passes
+- [ ]  Needed tests exist and passing or not needed
+- [ ]  The change is sufficiently small
+
+## For the reviewer
+
+- [ ] OK, code does what it's intended for
+- [ ] its' OK to do it that way
+- [ ] it's OK to read and comprehend the code
+- [ ] tests, documentation, style are OK

.github/workflows/r-build-check.yml

@@ -0,0 +1,10 @@
+name: r-build-check
+on:
+    pull_request:
+        branches: ['master', 'dev']
+    workflow_dispatch:
+
+jobs:
+    build-check:
+        uses: FertigLab/actions/.github/workflows/r-build-check.yml@v1
+        secrets: inherit

NEWS.md

@@ -1,3 +1,17 @@
+# dominoSignal v1.0.1
+
+## Receptor Complex Bugfix
+
+- Resolved issue where if create_domino was run with complexes=TRUE and no complexes were found to have active signaling, the full signaling matrix would be replaced by a NULL value.
+
+## GitHub Actions
+
+- Restoration of .github/workflows scripts for automatic build checks.
+
+# dominoSignal v1.0.0
+
+- Version number update to signify acceptance to bioconductor in release 3.20
+
 # dominoSignal v0.99.4
 
 ## Vignettes

R/processing_fxns.R

@@ -139,11 +139,12 @@ build_domino <- function(
         inc_ligs <- unlist(inc_ligs_list)
       }
       lig_genes <- intersect(inc_ligs, rownames(dom@z_scores))
-      if (length(lig_genes) %in% c(0, 1)) {
+      if (length(lig_genes) == 0) {
         lig_genes <- numeric(0)
       }
       cl_sig_mat <- matrix(0, ncol = length(levels(dom@clusters)), nrow = length(lig_genes))
       colnames(cl_sig_mat) <- colnames(signaling)
+      if (!identical(lig_genes, numeric(0))) {rownames(cl_sig_mat) <- lig_genes}
       rownames(cl_sig_mat) <- lig_genes
       for (c2 in levels(dom@clusters)) {
         n_cell <- length(which(dom@clusters == c2))
@@ -173,7 +174,7 @@ build_domino <- function(
           }
         })
         names(cl_sig_list) <- names(inc_ligs_list)
-        if (length(cl_sig_list) > 1) {
+        if (length(cl_sig_list) > 1 & !all(sapply(cl_sig_list, is.null))) {
           cl_sig_mat <- do.call(rbind, cl_sig_list)
         }
       }

R/utils.R

@@ -490,3 +490,43 @@ mock_linkage_summary <- function() {
 )
 return(linkage_sum_tiny)
 }
+
+#' Convert between ligand names and gene names
+#'
+#' @param dom A domino object
+#' @param genes A vector of genes on which to resolve ligand and gene names
+#'
+#' @return A vector of names where ligand names have been replaced with gene names if applicable
+#' @keywords internal
+resolve_names <- function(dom, genes) {
+  rl_map = dom@misc[["rl_map"]]
+  genes_resolved <- vapply(genes, FUN.VALUE = character(1), FUN = function(l){
+    int <- rl_map[rl_map$L.name == l, ][1,] 
+    if((int$L.name != int$L.gene) & !grepl("\\,", int$L.gene)){
+      int$L.gene
+    } else { 
+      int$L.name
+    }
+  })
+  return(genes_resolved)
+}
+
+#' Convert between complex names and gene names
+#'
+#' @param dom A domino object
+#' @param genes A vector of genes, some of which may be complexes
+#'
+#' @return A list where any complexes are mapped to a vector of
+#'   component genes. The list names are set to the input gene names.
+#' @keywords internal
+resolve_complexes <- function(dom, genes) {
+  genes_list <- lapply(genes, function(l){
+    if(l %in% names(dom@linkages$complexes)){
+      return(dom@linkages$complexes[[l]])
+    } else {
+      return(l)
+    }
+  })
+  names(genes_list) <- genes
+  return(genes_list)
+}

tests/testthat/test-utils.R

@@ -42,3 +42,44 @@ test_that("check_arg works for class", {
   expect_silent(check_arg(data.frame(a = c(1, 2), b = c(3, 4)),
                           allow_class = c("data.frame", "matrix")))
 })
+
+test_that("resolve_complexes maps complex names to their component genes, resolve_names maps ligand name to gene name", {
+  data(CellPhoneDB)
+  rl_map_tiny <- create_rl_map_cellphonedb(
+    genes = CellPhoneDB$genes_tiny,
+    proteins = CellPhoneDB$proteins_tiny,
+    interactions = CellPhoneDB$interactions_tiny,
+    complexes = CellPhoneDB$complexes_tiny)
+  entry_for_resolve_names <- c(int_pair = "12oxoLeukotrieneB4_byPTGR1 & LTB4R", 
+                               name_A = "12oxoLeukotrieneB4_byPTGR1", uniprot_A = "Q14914", gene_A = "PTGR1", type_A = "L", 
+                               name_B = "LTB4R", uniprot_B = "Q15722", gene_B = "LTB4R", type_B = "R", 
+                               annotation_strategy = "curated", 
+                               source = "HMRbase;uniprot;reactome", 
+                               database_name = "CellPhoneDB")
+  rl_map_tiny <- rbind(rl_map_tiny, entry_for_resolve_names)
+
+  data(SCENIC)
+  regulon_list_tiny <- create_regulon_list_scenic(
+    regulons = SCENIC$regulons_tiny)
+
+  data(PBMC)
+  pbmc_dom_tiny <- create_domino(
+    rl_map = rl_map_tiny, features = SCENIC$auc_tiny,
+    counts = PBMC$RNA_count_tiny, z_scores = PBMC$RNA_zscore_tiny,
+    clusters = PBMC$clusters_tiny, tf_targets = regulon_list_tiny,
+    use_clusters = TRUE, use_complexes = TRUE, remove_rec_dropout = FALSE)
+
+  # Test resolve_names
+  genes <- c("integrin_a6b4_complex", "TGFB3", "12oxoLeukotrieneB4_byPTGR1")
+  ligand_names_resolved <- c("integrin_a6b4_complex" = "integrin_a6b4_complex", 
+                             "TGFB3" = "TGFB3", 
+                             "12oxoLeukotrieneB4_byPTGR1" = "PTGR1")
+  expect_equal(resolve_names(pbmc_dom_tiny, genes), ligand_names_resolved)
+
+  # Test resolve_complexes
+  genes <- c("integrin_a6b4_complex", "IL7_receptor", "TGFBR3")
+  complexes_resolved <- list("integrin_a6b4_complex" = c("ITGB4", "ITGA6"),
+                             "IL7_receptor" = c("IL7R", "IL2RG"),
+                             "TGFBR3" = "TGFBR3")
+  expect_equal(resolve_complexes(pbmc_dom_tiny, genes), complexes_resolved)
+})