diff --git a/.Rbuildignore b/.Rbuildignore index 4c39292..b0b5819 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -5,3 +5,4 @@ ^Scratch\.RConsole$ ^README\.Rmd$ ^README\.html$ +^\.github$ diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..0f2fe08 --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,52 @@ +# 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] + +name: R-CMD-check + +permissions: read-all + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: macos-latest, r: 'release'} + - {os: windows-latest, r: 'release'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + 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: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml new file mode 100644 index 0000000..c0781e7 --- /dev/null +++ b/.github/workflows/check-bioc.yml @@ -0,0 +1,338 @@ +## Read more about GitHub actions the features of this GitHub Actions workflow +## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action +## +## For more details, check the biocthis developer notes vignette at +## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html +## +## You can add this workflow to other packages using: +## > biocthis::use_bioc_github_action() +## +## Using GitHub Actions exposes you to many details about how R packages are +## compiled and installed in several operating system.s +### If you need help, please follow the steps listed at +## https://github.com/r-lib/actions#where-to-find-help +## +## If you found an issue specific to biocthis's GHA workflow, please report it +## with the information that will make it easier for others to help you. +## Thank you! + +## Acronyms: +## * GHA: GitHub Action +## * OS: operating system + +on: + push: + pull_request: + +name: R-CMD-check-bioc + +## These environment variables control whether to run GHA code later on that is +## specific to testthat, covr, and pkgdown. +## +## If you need to clear the cache of packages, update the number inside +## cache-version as discussed at https://github.com/r-lib/actions/issues/86. +## Note that you can always run a GHA test without the cache by using the word +## "/nocache" in the commit message. +env: + has_testthat: 'true' + run_covr: 'true' + run_pkgdown: 'false' + has_RUnit: 'false' + cache-version: 'cache-v1' + run_docker: 'false' + +jobs: + build-check: + runs-on: ${{ matrix.config.os }} + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + container: ${{ matrix.config.cont }} + ## Environment variables unique to this job. + + strategy: + fail-fast: false + matrix: + config: + - { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } + - { os: macOS-latest, r: '4.4', bioc: '3.20'} + - { os: windows-latest, r: '4.4', bioc: '3.20'} + ## Check https://github.com/r-lib/actions/tree/master/examples + ## for examples using the http-user-agent + env: + R_REMOTES_NO_ERRORS_FROM_WARNINGS: true + RSPM: ${{ matrix.config.rspm }} + NOT_CRAN: true + TZ: UTC + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + + steps: + + ## Set the R library to the directory matching the + ## R packages cache step further below when running on Docker (Linux). + - name: Set R Library home on Linux + if: runner.os == 'Linux' + run: | + mkdir /__w/_temp/Library + echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile + + ## Most of these steps are the same as the ones in + ## 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@v3 + + ## R is already included in the Bioconductor docker images + - name: Setup R from r-lib + if: runner.os != 'Linux' + uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + + ## pandoc is already included in the Bioconductor docker images + - name: Setup pandoc from r-lib + if: runner.os != 'Linux' + uses: r-lib/actions/setup-pandoc@v2 + + - name: Query dependencies + run: | + install.packages('remotes') + saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) + shell: Rscript {0} + + - name: Restore R package cache + if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'" + uses: actions/cache@v3 + with: + path: ${{ env.R_LIBS_USER }} + key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4- + + - name: Cache R packages on Linux + if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' " + uses: actions/cache@v3 + with: + path: /home/runner/work/_temp/Library + key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4- + + # - name: Install Linux system dependencies + # if: runner.os == 'Linux' + # run: | + # sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))') + # echo $sysreqs + # sudo -s eval "$sysreqs" + + - name: Install macOS system dependencies + if: matrix.config.os == 'macOS-latest' + run: | + ## Enable installing XML from source if needed + brew install libxml2 + echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV + + ## Required to install magick as noted at + ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 + brew install imagemagick@6 + + ## For textshaping, required by ragg, and required by pkgdown + brew install harfbuzz fribidi + + ## For installing usethis's dependency gert + brew install libgit2 + + ## Required for tcltk + brew install xquartz --cask + + - name: Install Windows system dependencies + if: runner.os == 'Windows' + run: | + ## Edit below if you have any Windows system dependencies + shell: Rscript {0} + + - name: Install BiocManager + run: | + message(paste('****', Sys.time(), 'installing BiocManager ****')) + remotes::install_cran("BiocManager") + shell: Rscript {0} + + - name: Set BiocVersion + run: | + BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE) + shell: Rscript {0} + + - name: Install dependencies pass 1 + run: | + ## Try installing the package dependencies in steps. First the local + ## dependencies, then any remaining dependencies to avoid the + ## issues described at + ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html + ## https://github.com/r-lib/remotes/issues/296 + ## Ideally, all dependencies should get installed in the first pass. + + ## For running the checks + message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) + install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories()) + + ## Pass #1 at installing dependencies + message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****')) + 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 + 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} + + - name: Install BiocGenerics + if: env.has_RUnit == 'true' + run: | + ## Install BiocGenerics + BiocManager::install("BiocGenerics") + shell: Rscript {0} + + - name: Install covr + 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/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' + run: | + remotes::install_github("r-lib/pkgdown") + shell: Rscript {0} + + - name: Session info + run: | + options(width = 100) + pkgs <- installed.packages()[, "Package"] + sessioninfo::session_info(pkgs, include_base = TRUE) + shell: Rscript {0} + + - name: Run CMD check + env: + _R_CHECK_CRAN_INCOMING_: false + DISPLAY: 99.0 + run: | + options(crayon.enabled = TRUE) + rcmdcheck::rcmdcheck( + args = c("--no-manual", "--no-vignettes", "--timings"), + build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"), + error_on = "warning", + check_dir = "check" + ) + shell: Rscript {0} + + ## Might need an to add this to the if: && runner.os == 'Linux' + - name: Reveal testthat details + if: env.has_testthat == 'true' + run: find . -name testthat.Rout -exec cat '{}' ';' + + - name: Run RUnit tests + if: env.has_RUnit == 'true' + run: | + BiocGenerics:::testPackage() + shell: Rscript {0} + + - name: Run BiocCheck + env: + DISPLAY: 99.0 + run: | + BiocCheck::BiocCheck( + dir('check', 'tar.gz$', full.names = TRUE), + `quit-with-status` = TRUE, + `no-check-R-ver` = TRUE, + `no-check-bioc-help` = TRUE + ) + shell: Rscript {0} + + - name: Test coverage + if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' + run: | + covr::codecov(coverage = covr::package_coverage(type = "all")) + shell: Rscript {0} + + - name: Install package + if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' + run: R CMD INSTALL . + + - 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: ${{ runner.os }}-biocversion-devel-r-4.4-results + path: check + + + ## Code adapted from + ## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92 + docker-build-and-push: + runs-on: ubuntu-latest + needs: build-check + steps: + - name: Checkout Repository + if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" + uses: actions/checkout@v3 + + - name: Register repo name + if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" + id: reg_repo_name + run: | + echo CONT_IMG_NAME=$(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: + context: . + push: true + tags: > + ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest, + ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml new file mode 100644 index 0000000..d1f7650 --- /dev/null +++ b/.github/workflows/pr-commands.yaml @@ -0,0 +1,81 @@ +# 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: + issue_comment: + types: [created] + +name: Commands + +permissions: read-all + +jobs: + document: + if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }} + name: document + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/pr-fetch@v2 + with: + repo-token: ${{ secrets.GITHUB_TOKEN }} + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::roxygen2 + needs: pr-document + + - name: Document + run: roxygen2::roxygenise() + shell: Rscript {0} + + - name: commit + run: | + git config --local user.name "$GITHUB_ACTOR" + git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" + git add man/\* NAMESPACE + git commit -m 'Document' + + - uses: r-lib/actions/pr-push@v2 + with: + repo-token: ${{ secrets.GITHUB_TOKEN }} + + style: + if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }} + name: style + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/pr-fetch@v2 + with: + repo-token: ${{ secrets.GITHUB_TOKEN }} + + - uses: r-lib/actions/setup-r@v2 + + - name: Install dependencies + run: install.packages("styler") + shell: Rscript {0} + + - name: Style + run: styler::style_pkg() + shell: Rscript {0} + + - name: commit + run: | + git config --local user.name "$GITHUB_ACTOR" + git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" + git add \*.R + git commit -m 'Style' + + - uses: r-lib/actions/pr-push@v2 + with: + repo-token: ${{ secrets.GITHUB_TOKEN }} diff --git a/DESCRIPTION b/DESCRIPTION index ab5886f..01c47d8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,12 +1,13 @@ Package: eheat Title: Extented ComplexHeatmap -Version: 0.0.0.9000 +Version: 0.99.0 Authors@R: - person("Yun", "Peng", , "yunyunp96@gmail.com", role = c("aut", "cre")) -Description: Extented ComplexHeatmap. + person("Yun", "Peng", , "yunyunp96@163.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2801-3332")) +Description: This package serves as a bridge between the ggplot2 and ComplexHeatmap packages. Essentially, all ggplot2 geometries and operations can be utilized in ComplexHeatmap. URL: https://github.com/Yunuuuu/eheat BugReports: https://github.com/Yunuuuu/eheat/issues License: MIT + file LICENSE +biocViews: Software, Visualization Encoding: UTF-8 Depends: ComplexHeatmap, diff --git a/R/gganno.R b/R/gganno.R index de5df79..99ed9a0 100644 --- a/R/gganno.R +++ b/R/gganno.R @@ -31,9 +31,10 @@ #' draw(gganno(rnorm(10L), function(p) { #' p + geom_point(aes(y = V1)) #' }, height = unit(10, "cm"), width = unit(0.7, "npc"))) -#' draw(gganno2(rnorm(10L), function(p) { -#' p + geom_point(aes(y = V1)) -#' }, height = unit(10, "cm"), width = unit(0.7, "npc"))) +#' @return +#' - `gganno`: A `ggAnnotationFunction` object. +#' - `gganno2`: A [AnnotationFunction][ComplexHeatmap::AnnotationFunction] +#' object. #' @export #' @name gganno gganno <- function(matrix, ggfn, ..., which = NULL, @@ -57,6 +58,10 @@ gganno <- function(matrix, ggfn, ..., which = NULL, out } +#' @examples +#' draw(gganno2(rnorm(10L), function(p) { +#' p + geom_point(aes(y = V1)) +#' }, height = unit(10, "cm"), width = unit(0.7, "npc"))) #' @export #' @rdname gganno gganno2 <- function( diff --git a/R/ggheat.R b/R/ggheat.R index f158372..5868a28 100644 --- a/R/ggheat.R +++ b/R/ggheat.R @@ -212,6 +212,8 @@ ggheat <- function(matrix, ggfn = NULL, ..., ggparams = list(), debug = FALSE) { out } +#' @examples +#' draw(ggheat(matrix(rnorm(81), nrow = 9))) #' @importFrom ComplexHeatmap draw #' @export ComplexHeatmap::draw diff --git a/R/utils-complexheatmap.R b/R/utils-complexheatmap.R index 30609e4..cf4ccc9 100644 --- a/R/utils-complexheatmap.R +++ b/R/utils-complexheatmap.R @@ -1,3 +1,5 @@ +#' @examples +#' ht_opt("heatmap_row_names_gp") #' @importFrom ComplexHeatmap ht_opt #' @export ComplexHeatmap::ht_opt diff --git a/R/utils.R b/R/utils.R index 6859543..2e4a356 100644 --- a/R/utils.R +++ b/R/utils.R @@ -4,10 +4,14 @@ pkg_nm <- function() { utils::packageName(topenv(environment())) } +#' @examples +#' gpar(col = "red") #' @importFrom grid gpar #' @export grid::gpar +#' @examples +#' unit(1, "npc") #' @importFrom grid unit #' @export grid::unit diff --git a/README.Rmd b/README.Rmd index 8bf4d53..588968e 100644 --- a/README.Rmd +++ b/README.Rmd @@ -16,6 +16,7 @@ knitr::opts_chunk$set( # eheat +[![R-CMD-check](https://github.com/Yunuuuu/eheat/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Yunuuuu/eheat/actions/workflows/R-CMD-check.yaml) ```{r child = "vignettes/eheat.Rmd"} diff --git a/man/eheat-package.Rd b/man/eheat-package.Rd index dbd4f00..32313cc 100644 --- a/man/eheat-package.Rd +++ b/man/eheat-package.Rd @@ -6,7 +6,7 @@ \alias{eheat-package} \title{eheat: Extented ComplexHeatmap} \description{ -Extented ComplexHeatmap. +This package serves as a bridge between the ggplot2 and ComplexHeatmap packages. Essentially, all ggplot2 geometries and operations can be utilized in ComplexHeatmap. } \seealso{ Useful links: @@ -17,7 +17,7 @@ Useful links: } \author{ -\strong{Maintainer}: Yun Peng \email{yunyunp96@gmail.com} +\strong{Maintainer}: Yun Peng \email{yunyunp96@163.com} (\href{https://orcid.org/0000-0003-2801-3332}{ORCID}) } \keyword{internal} diff --git a/man/gganno.Rd b/man/gganno.Rd index 4108ff1..6ca7247 100644 --- a/man/gganno.Rd +++ b/man/gganno.Rd @@ -59,6 +59,12 @@ be deemed acceptable) to be carried out conjointly with the } \value{ A \code{ggAnnotationFunction} object. + +\itemize{ +\item \code{gganno}: A \code{ggAnnotationFunction} object. +\item \code{gganno2}: A \link[ComplexHeatmap:AnnotationFunction]{AnnotationFunction} +object. +} } \description{ Plot heatmaps layer by layer diff --git a/man/reexports.Rd b/man/reexports.Rd index 7fda3db..272aa97 100644 --- a/man/reexports.Rd +++ b/man/reexports.Rd @@ -8,6 +8,12 @@ \alias{gpar} \alias{unit} \title{Objects exported from other packages} +\examples{ +draw(ggheat(matrix(rnorm(81), nrow = 9))) +ht_opt("heatmap_row_names_gp") +gpar(col = "red") +unit(1, "npc") +} \keyword{internal} \description{ These objects are imported from other packages. Follow the links