merge devel changes into c++Merge

.BBSoptions

@@ -0,0 +1,3 @@
+# .BBSoptions should contain UnsupportedPlatforms: win32, as builds on Windows 32-bit are not supported.
+# https://www.bioconductor.org/packages/release/bioc/vignettes/basilisk/inst/doc/motivation.html#setting-up-the-package
+UnsupportedPlatforms: win32

.Rbuildignore

@@ -8,3 +8,4 @@
 ^doc$
 ^Meta$
 ^\.github$
+^data-raw$

.github/workflows/check-bioc.yml

@@ -52,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.2', bioc: '3.16'}
-          # - { os: windows-latest, r: '4.2', bioc: '3.16'}
+          - { os: ubuntu-latest, r: '4.3', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
+          - { os: macOS-latest, r: '4.3', bioc: '3.17'}
+          # - { os: windows-latest, r: '4.3', bioc: '3.17'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -79,7 +79,7 @@ jobs:
       ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
       ## If they update their steps, we will also need to update ours.
       - name: Checkout Repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
@@ -102,19 +102,19 @@ jobs:
 
       - name: Restore R package cache
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
@@ -170,35 +170,19 @@ jobs:
           ## https://github.com/r-lib/remotes/issues/296
           ## Ideally, all dependencies should get installed in the first pass.
 
-          ## Set the repos source depending on the OS
-          ## Alternatively use https://storage.googleapis.com/bioconductor_docker/packages/
-          ## though based on https://bit.ly/bioc2021-package-binaries
-          ## the Azure link will be the main one going forward.
-          gha_repos <- if(
-              .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
-          ) c(
-              "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.16/bioc",
-              BiocManager::repositories()
-              ) else BiocManager::repositories()
-
           ## For running the checks
           message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
-          install.packages(c("rcmdcheck", "BiocCheck"), repos = gha_repos)
+          install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())
 
           ## Pass #1 at installing dependencies
-          ## This pass uses AnVIL-powered fast binaries
-          ## details at https://github.com/nturaga/bioc2021-bioconductor-binaries
-          ## The speed gains only apply to the docker builds.
           message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
-          remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = TRUE)
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
         continue-on-error: true
         shell: Rscript {0}
 
       - name: Install dependencies pass 2
         run: |
           ## Pass #2 at installing dependencies
-          ## This pass does not use AnVIL and will thus update any packages
-          ## that have seen been updated in Bioconductor
           message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
           remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
         shell: Rscript {0}
@@ -211,13 +195,13 @@ jobs:
         shell: Rscript {0}
 
       - name: Install covr
-        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
           remotes::install_cran("covr")
         shell: Rscript {0}
 
       - name: Install pkgdown
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
           remotes::install_cran("pkgdown")
         shell: Rscript {0}
@@ -238,7 +222,7 @@ jobs:
           rcmdcheck::rcmdcheck(
               args = c("--no-manual", "--no-vignettes", "--timings"),
               build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
-              error_on = "error",
+              error_on = "warning",
               check_dir = "check"
           )
         shell: Rscript {0}
@@ -267,46 +251,89 @@ jobs:
         shell: Rscript {0}
 
       - name: Test coverage
-        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
           covr::codecov()
         shell: Rscript {0}
 
       - name: Install package
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: R CMD INSTALL .
 
-      - name: Build and deploy pkgdown site
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
-          Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
-        shell: bash {0}
+      - name: Build pkgdown site
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
         ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
         ## at least one locally before this will work. This creates the gh-pages
         ## branch (erasing anything you haven't version controlled!) and
         ## makes the git history recognizable by pkgdown.
 
+      - name: Install deploy dependencies
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: |
+          apt-get update && apt-get -y install rsync
+
+      - name: Deploy pkgdown site to GitHub pages 🚀
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        uses: JamesIves/github-pages-deploy-action@releases/v4
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
+
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-results
+          name: ${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-results
           path: check
 
-        ## Note that DOCKER_PASSWORD is really a token for your dockerhub
-        ## account, not your actual dockerhub account password.
-        ## This comes from
-        ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html#6-add-secrets-to-github-repo
-        ## Check https://github.com/docker/build-push-action/tree/releases/v1
-        ## for more details.
-      - uses: docker/build-push-action@v1
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "
+
+  ## Code adapted from
+  ## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92
+  docker-build-and-push:
+    runs-on: ubuntu-latest
+    needs: build-check
+    steps:
+      - name: Checkout Repository
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        uses: actions/checkout@v3
+
+      - name: Register repo name
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        id: reg_repo_name
+        run: |
+          echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
+
+      - name: Set up QEMU
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        uses: docker/setup-qemu-action@v2
+
+      - name: Set up Docker Buildx
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        uses: docker/setup-buildx-action@v2
+
+      - name: Login to Docker Hub
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      ## Note that DOCKERHUB_TOKEN is really a token for your dockerhub
+      ## account, not your actual dockerhub account password. You can get it
+      ## from https://hub.docker.com/settings/security.
+      ## Check https://github.com/docker/build-push-action/tree/v4.0.0
+      ## for more details.
+      ## Alternatively, try checking
+      ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html.
+
+      - name: Build and Push Docker
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()"
+        uses: docker/build-push-action@v4
         with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-          repository: olivervoogd/flames
-          tag_with_ref: true
-          tag_with_sha: true
-          tags: latest
+          context: .
+          push: true
+          tags: >
+            ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest,
+            ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: FLAMES
 Type: Package
 Title: FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data
-Version: 1.7.3
+Version: 1.7.5
 Date: 2023-10-2
 Authors@R: c(
        person("Luyi", "Tian", role=c("aut"),
@@ -27,7 +27,6 @@ biocViews: RNASeq, SingleCell, Transcriptomics, DataImport,
 License: GPL (>= 2)
 Encoding: UTF-8
 Imports: 
-    arrangements,
     basilisk,
     bambu,
     Biostrings,
@@ -87,3 +86,7 @@ RoxygenNote: 7.2.3
 VignetteBuilder: knitr
 URL: https://github.com/OliverVoogd/FLAMES
 Config/testthat/edition: 3
+Depends: 
+    R (>= 2.10)
+LazyData: true
+StagedInstall: no

NAMESPACE

@@ -22,11 +22,11 @@ export(plot_coverage)
 export(plot_demultiplex)
 export(quantify_transcript)
 export(sc_DTU_analysis)
-export(sc_annotate_plots)
 export(sc_heatmap_expression)
 export(sc_long_multisample_pipeline)
 export(sc_long_pipeline)
 export(sc_mutations)
+export(sc_reduce_dims)
 export(sc_umap_expression)
 import(zlibbioc)
 importFrom(BiocGenerics,cbind)
@@ -38,7 +38,6 @@ importFrom(Biostrings,readDNAStringSet)
 importFrom(Biostrings,writeXStringSet)
 importFrom(ComplexHeatmap,AnnotationFunction)
 importFrom(ComplexHeatmap,Heatmap)
-importFrom(ComplexHeatmap,HeatmapAnnotation)
 importFrom(ComplexHeatmap,columnAnnotation)
 importFrom(ComplexHeatmap,rowAnnotation)
 importFrom(DropletUtils,read10xCounts)
@@ -55,7 +54,6 @@ importFrom(GenomicRanges,granges)
 importFrom(GenomicRanges,strand)
 importFrom(GenomicRanges,width)
 importFrom(Matrix,colSums)
-importFrom(Matrix,t)
 importFrom(Matrix,tail)
 importFrom(MultiAssayExperiment,"experiments<-")
 importFrom(MultiAssayExperiment,MultiAssayExperiment)
@@ -86,14 +84,11 @@ importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)
 importFrom(SummarizedExperiment,rowRanges)
-importFrom(arrangements,combinations)
 importFrom(bambu,bambu)
 importFrom(bambu,prepareAnnotations)
 importFrom(bambu,writeToGTF)
 importFrom(basilisk,BasiliskEnvironment)
 importFrom(basilisk,basiliskRun)
-importFrom(basilisk,basiliskStart)
-importFrom(basilisk,basiliskStop)
 importFrom(circlize,colorRamp2)
 importFrom(cowplot,get_legend)
 importFrom(cowplot,plot_grid)
@@ -117,7 +112,6 @@ importFrom(dplyr,ungroup)
 importFrom(future,plan)
 importFrom(ggbio,autoplot)
 importFrom(ggbio,geom_alignment)
-importFrom(ggbio,xlim)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,coord_polar)
 importFrom(ggplot2,element_blank)
@@ -137,6 +131,7 @@ importFrom(ggplot2,scale_colour_gradient2)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,xlab)
+importFrom(ggplot2,xlim)
 importFrom(ggplot2,ylab)
 importFrom(grid,unit)
 importFrom(grid,viewport)
@@ -145,22 +140,22 @@ importFrom(igraph,as_adjacency_matrix)
 importFrom(jsonlite,fromJSON)
 importFrom(jsonlite,toJSON)
 importFrom(magrittr,"%>%")
-importFrom(magrittr,'%>%')
 importFrom(methods,is)
 importFrom(parallel,detectCores)
 importFrom(reticulate,dict)
 importFrom(reticulate,import_from_path)
 importFrom(rtracklayer,import)
-importFrom(rtracklayer,import.gff3)
 importFrom(scater,runUMAP)
 importFrom(scran,buildSNNGraph)
 importFrom(scran,fixedPCA)
 importFrom(scran,getTopHVGs)
 importFrom(scran,modelGeneVar)
 importFrom(scuttle,addPerCellQC)
 importFrom(scuttle,addPerFeatureQC)
+importFrom(scuttle,computeLibraryFactors)
 importFrom(scuttle,isOutlier)
 importFrom(scuttle,logNormCounts)
+importFrom(scuttle,quickPerCellQC)
 importFrom(stats,chisq.test)
 importFrom(stats,complete.cases)
 importFrom(stats,median)
@@ -179,6 +174,7 @@ importFrom(utils,read.csv)
 importFrom(utils,read.delim)
 importFrom(utils,read.table)
 importFrom(utils,setTxtProgressBar)
+importFrom(utils,txtProgressBar)
 importFrom(utils,write.csv)
 importFrom(withr,with_package)
 useDynLib(FLAMES, .registration=TRUE)

R/BLAZE_demultiplexing.R

@@ -21,12 +21,12 @@
 #' fastq1 <- bfc[[names(BiocFileCache::bfcadd(bfc, 'Fastq1', fastq1_url))]]
 #' outdir <- tempfile()
 #' dir.create(outdir)
-#' config = jsonlite::fromJSON(system.file('extdata/template_config.json', package = 'FLAMES'))
-#' config$blaze_parameters['output-prefix'] <- outdir
 #' \dontrun{
-#'    blaze(config$blaze_parameters, fastq1)
-#' }
+#' blaze(expect_cells=10, fastq1, overwrite=TRUE)
+#' } 
+#'
 #' @importFrom reticulate import_from_path dict
+#' @importFrom basilisk basiliskRun
 #' @export
 blaze <- function(expect_cells, fq_in, ...) {
         # prepare command-line-style arguments for blaze        
@@ -39,7 +39,7 @@ blaze <- function(expect_cells, fq_in, ...) {
         if (length(blaze_config) > 0) {
             # handle the switch options first as they do not have values
             if ('overwrite' %in% names(blaze_config) && blaze_config$`overwrite` == TRUE) {
-                blaze_argv <- paste(blaze_argv, '--overwrite ')
+                blaze_argv <- paste(blaze_argv, '--overwrite --minimal_stdout ')
             }
 
             print(blaze_config)
@@ -60,7 +60,7 @@ blaze <- function(expect_cells, fq_in, ...) {
 
         # run blaze
         ret <-
-            callBasilisk(flames_env, function(blaze_argv) {
+            basiliskRun(env = flames_env, fun = function(blaze_argv) {
                 # blaze_path <- system.file("blaze", package = "FLAMES")
                 cat("Running BLAZE...\n")
                 cat("Argument: ", blaze_argv, "\n")