Merge pull request #116 from FertigLab/dev

update master to 0.99.2

.Rbuildignore

@@ -18,3 +18,6 @@
 ^old\.README\.md$
 ^readme_images$
 ^scenic_bash$
+^vignettes/articles$
+.nojekyll$
+

.github/.gitignore

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

.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

@@ -1,4 +1,22 @@
 name: Update Bioconductor package files
 
 on:
-  workflow_dispatch:
+  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

@@ -1,3 +1,43 @@
-name: documentation-update
+# 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:
-    workflow_dispatch:
+    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

@@ -1,3 +1,48 @@
-name: pkgdown-update
+# 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:
-    workflow_dispatch:
+  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@v3
+
+      - 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

@@ -6,6 +6,7 @@ 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
 

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

@@ -1,9 +1,7 @@
 name: r-build-check
 on:
-    push:
-        branches: ['v0.2.2_development']
     pull_request:
-        branches: ['master', 'v0.2.2']
+        branches: ['master', 'dev']
     workflow_dispatch:
 
 jobs:

.gitignore

@@ -10,6 +10,3 @@ R/.Rhistory
 scenic/*
 
 scratch/
-
-.github/workflows/doc_update.yml
-.github/workflows/pkgdown_update.yml

.nojekyll

@@ -0,0 +1 @@
+

DESCRIPTION

@@ -1,6 +1,6 @@
-Package: domino2
+Package: dominoSignal
 Title: Cell Communication Analysis for Single Cell RNA Sequencing
-Version: 0.99.1
+Version: 0.99.2
 Authors@R: c(
     person("Christopher", "Cherry", role = c("aut"), email = "[email protected]", comment = c(ORCID = "0000-0002-5481-0055")),
     person("Jacob T", "Mitchell", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0002-5370-9692")),
@@ -11,8 +11,8 @@ Authors@R: c(
     person("Jennifer", "Elisseeff", role = "ctb", email = "[email protected]", comment = c(ORCID = "0000-0002-5066-1996"))
     )
 Description: 
-    Domino2 is a package developed to analyze cell signaling through ligand - receptor - transcription factor networks in scRNAseq data. It takes as input information transcriptomic data, requiring counts, z-scored counts, and cluster labels, as well as information on transcription factor activation (such as from SCENIC) and a database of ligand and receptor pairings (such as from cellphoneDB). This package creates an object storing ligand - receptor - transcription factor linkages by cluster and provides several methods for exploring, summarizing, and visualizing the analysis.
-BugReports: https://github.com/FertigLab/domino2/issues
+    dominoSignal is a package developed to analyze cell signaling through ligand - receptor - transcription factor networks in scRNAseq data. It takes as input information transcriptomic data, requiring counts, z-scored counts, and cluster labels, as well as information on transcription factor activation (such as from SCENIC) and a database of ligand and receptor pairings (such as from cellphoneDB). This package creates an object storing ligand - receptor - transcription factor linkages by cluster and provides several methods for exploring, summarizing, and visualizing the analysis.
+BugReports: https://github.com/FertigLab/dominoSignal/issues
 Depends:
     R(>= 4.2.0),
 Imports:
@@ -31,7 +31,7 @@ Imports:
 License: GPL-3 | file LICENSE
 Encoding: UTF-8
 LazyData: false
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 biocViews:
     SystemsBiology,
     SingleCell,
@@ -43,7 +43,10 @@ Suggests:
     rmarkdown,
     Seurat,
     testthat,
-    formatR
+    formatR,
+    BiocFileCache,
+    SingleCellExperiment
 VignetteBuilder: knitr
 Language: en-US
 Roxygen: list(markdown = TRUE)
+URL: https://fertiglab.github.io/dominoSignal/

NEWS.md

@@ -1,4 +1,22 @@
-# domino2 v0.2.2
+# dominoSignal v0.99.2
+
+## Package Name
+
+- Update of package name from "domino2" to "dominoSignal"
+
+## Bioconductor Standards
+
+- Update to Vignettes presenting application of the DominoSignal pipeline on data formatted as a SingleCellExperiment object
+- Implemented caching of example data by BiocCache to meet package size limits
+- Removal of depreciated scripts for running SCENIC. Tutorials for running SCENIC are still present in vignettes
+- Corrected BiocCheck notes pertaining to coding practices including paste in conditional statements, functions with dontrun examples, usage of seq_len or seq_along in place of seq, and usage of vapply in place of sapply
+
+
+# dominoSignal v0.99.1
+
+- Update to Bioconductor version numbering conventions for package submission
+
+# dominoSignal v0.2.2
 
 ## Linkage functions
 - Addition of new class to summarize linkages in objects
@@ -8,7 +26,7 @@
 ## Package structure
 - Adjustments made to meet BioConductor standards
 
-# domino2 v0.2.1
+# dominoSignal v0.2.1
 
 ## Updates to domino object construction
 - Uniform formats for inputs of receptor-ligand interaction databases, transcription factor activity features, and regulon gene lists for operability with alternative databases and transcription factor activation inference methods

R/class_definitions.R

@@ -23,6 +23,7 @@ NULL
 #' @name domino-class
 #' @rdname domino-class
 #' @exportClass domino
+#' @return an instance of class `domino `
 #'
 domino <- methods::setClass(
   Class = "domino",
@@ -58,6 +59,7 @@ domino <- methods::setClass(
 #' @name linkage_summary-class
 #' @rdname linkage_summary-class
 #' @exportClass linkage_summary
+#' @return an instance of class `linkage_summary`
 #'
 linkage_summary <- setClass(
   Class = "linkage_summary",
@@ -76,7 +78,7 @@ linkage_summary <- setClass(
 #' @return a printed description of the number of cell clusters in the object
 #' @keywords internal
 #' @examples
-#' print(domino2:::pbmc_dom_built_tiny)
+#' print(dominoSignal:::pbmc_dom_built_tiny)
 #' 
 setMethod("print", "domino", function(x, ...) {
   if (x@misc$build) {
@@ -103,9 +105,9 @@ setMethod("print", "domino", function(x, ...) {
 #' @return a printed description of the number of cells in a domino object and its build status
 #' @keywords internal
 #' @examples
-#' domino2:::pbmc_dom_built_tiny
+#' dominoSignal:::pbmc_dom_built_tiny
 #' 
-#' show(domino2:::pbmc_dom_built_tiny)
+#' show(dominoSignal:::pbmc_dom_built_tiny)
 #' 
 setMethod("show", "domino", function(object) {
   if (object@misc$build) {

R/convenience_fxns.R

@@ -15,39 +15,64 @@ NULL
 #'
 #' @param dom Domino object to rename clusters in
 #' @param clust_conv Named vector of conversions from old to new clusters. Values are taken as new clusters IDs and names as old cluster IDs.
+#' @param warning Logical. If TRUE, will warn if a cluster is not found in the conversion table. Default is FALSE.
 #' @return A domino object with clusters renamed in all applicable slots.
-#' @keywords internal
 #' @export
 #' @examples 
 #' new_clust <- c("CD8_T_cell" = "CD8+ T Cells",
 #'  "CD14_monocyte" = "CD14+ Monocytes", "B_cell" = "B Cells")
-#' pbmc_dom_built_tiny <- rename_clusters(domino2:::pbmc_dom_built_tiny, new_clust)
+#' pbmc_dom_built_tiny <- rename_clusters(dominoSignal:::pbmc_dom_built_tiny, new_clust)
 #'
-rename_clusters <- function(dom, clust_conv) {
-  if (is.null(dom@clusters)) {
-    stop("There are no clusters in this domino object")
-  }
-  if (dom@misc$create) {
-    dom@clusters <- revalue(dom@clusters, clust_conv)
-    colnames(dom@clust_de) <- clust_conv
-    names(colnames(dom@clust_de)) <- c()
-    colnames(dom@misc$cl_rec_percent) <- clust_conv
-  }
-  if (dom@misc$build) {
-    names(dom@linkages$clust_tf) <- clust_conv
-    names(dom@linkages$clust_rec) <- clust_conv
-    names(dom@linkages$clust_incoming_lig) <- clust_conv
-    names(dom@linkages$clust_tf_rec) <- clust_conv
-    colnames(dom@signaling) <- paste0("L_", clust_conv)
-    rownames(dom@signaling) <- paste0("R_", clust_conv)
-    names(dom@cl_signaling_matrices) <- clust_conv
-    for (cl in clust_conv) {
-      colnames(dom@cl_signaling_matrices[[cl]]) <- paste0("L_", clust_conv)
+rename_clusters <- function(dom, clust_conv, warning = FALSE) {
+    if (is.null(dom@clusters)) {
+        stop("There are no clusters in this domino object")
     }
-  }
-  return(dom)
+    if (dom@misc$create) {
+        dom@clusters <- plyr::revalue(dom@clusters, clust_conv, warn_missing = warning)
+        colnames(dom@clust_de) <- plyr::revalue(colnames(dom@clust_de), clust_conv, warn_missing = warning)
+        names(colnames(dom@clust_de)) <- c()
+        colnames(dom@misc$cl_rec_percent) <- plyr::revalue(colnames(dom@misc$cl_rec_percent),
+            clust_conv,
+            warn_missing = warning
+        )
+    }
+    if (dom@misc$build) {
+        names(dom@linkages$clust_tf) <- plyr::revalue(names(dom@linkages$clust_tf), clust_conv, warn_missing = warning)
+        names(dom@linkages$clust_rec) <- plyr::revalue(names(dom@linkages$clust_rec), clust_conv, warn_missing = warning)
+        names(dom@linkages$clust_incoming_lig) <- plyr::revalue(names(dom@linkages$clust_incoming_lig),
+            clust_conv,
+            warn_missing = warning
+        )
+        names(dom@linkages$clust_tf_rec) <- plyr::revalue(names(dom@linkages$clust_tf_rec),
+            clust_conv,
+            warn_missing = warning
+        )
+        sig_ligands <- colnames(dom@signaling)
+        sig_rec <- rownames(dom@signaling)
+        # Remove L_ prefix
+        sig_ligand_clust <- gsub("^L_", "", sig_ligands)
+        # Remove R_ prefix
+        sig_rec_clust <- gsub("^R_", "", sig_rec)
+        new_lig_clust <- plyr::revalue(sig_ligand_clust, clust_conv, warn_missing = warning)
+        new_rec_clust <- plyr::revalue(sig_rec_clust, clust_conv, warn_missing = warning)
+        colnames(dom@signaling) <- paste0("L_", new_lig_clust)
+        rownames(dom@signaling) <- paste0("R_", new_rec_clust)
+        names(dom@cl_signaling_matrices) <- plyr::revalue(names(dom@cl_signaling_matrices),
+            clust_conv,
+            warn_missing = warning
+        )
+        for (cl in names(dom@cl_signaling_matrices)) {
+            cl_sig_ligands <- colnames(dom@cl_signaling_matrices[[cl]])
+            # Remove L_ prefix
+            cl_sig_lig_clust <- gsub("^L_", "", cl_sig_ligands)
+            cl_sig_lig_new <- plyr::revalue(cl_sig_lig_clust, clust_conv, warn_missing = warning)
+            colnames(dom@cl_signaling_matrices[[cl]]) <- paste0("L_", cl_sig_lig_new)
+        }
+    }
+    return(dom)
 }
 
+
 #' Convert Genes Using Table
 #'
 #' Takes a vector of gene inputs and a conversion table  and returns a