Add GC content function for plot.

.Rbuildignore

@@ -3,3 +3,10 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.github$
+^doc$
+^Meta$
+^R-deprecated$
+^data-raw$
+^pkgdown$
+^LICENSE.md$
+^\.vscode$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,74 @@
+on:
+  push:
+    branches: master
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 4.3.1
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get install --yes libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev
+
+      - name: Install XQuartz
+        if: runner.os == 'macOS'
+        run: brew cask install xquartz
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ubuntu-r-4.0-4-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ubuntu-r-4.0-4-
+
+      - name: Install dependencies
+        run: |
+          install.packages("BiocManager")
+          BiocManager::install("IRanges")
+          BiocManager::install("ggtree")
+          install.packages("remotes")
+          remotes::install_deps(dependencies = TRUE)
+          install.packages('pkgdown')
+          install.packages('devtools')
+          remotes::install_dev("dplyr")
+          install.packages("Hmisc")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Session Info
+        run: |
+          library(gggenomes)
+          print(sessionInfo())
+        shell: Rscript {0}
+
+#      - name: Setup upterm session
+#        uses: lhotari/action-upterm@v1
+
+      - name: Configure git user
+        run: |
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+
+      - name: Deploy package
+        run: pkgdown::deploy_to_branch(new_process = FALSE, lazy=FALSE)
+        shell: Rscript {0}

.github/workflows/rhub.yaml

@@ -0,0 +1,97 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-tinytex@v2
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

.gitignore

@@ -1,3 +1,15 @@
 .Rproj.user
 .Rhistory
 .RData
+docs/
+org/
+R-deprecated/
+data-raw/
+tests/
+vignettes-manual-export/
+/doc/
+/Meta/
+gggenomes.Rcheck
+.vscode
+gggenomes_*.tar.gz
+vignettes/gggenomes_cache

DESCRIPTION

@@ -1,31 +1,51 @@
 Package: gggenomes
 Title: A Grammar of Graphics for Comparative Genomics
-Version: 0.0.0.9000
+Version: 1.0.1
 Authors@R: c(
-  person("Thomas", "Hackl", email = "thackl@lim4.de", role = c("aut", "cre")),
+  person("Thomas", "Hackl", email = "t.hackl@rug.nl", role = c("aut", "cre")),
   person("Markus J.", "Ankenbrand", email = "iimog@iimog.org", role = c("aut")),
+  person("Bart", "van Adrichem", role = c("aut")),
   person("Kristina", "Haslinger", email = "k.haslinger@rug.nl", role = c("ctb", "sad")))
-Description: gggenomes is an extension of ggplot2 for creating complex genomic
- maps. It builds on the power of ggplot2 and tidyverse adding new ggplot-style
- geoms & positions and dplyr-style verbs to manipulate the underlying data. It
- implements a layout concept inspired by ggraph and introduces tracks to bring
- tidyness to the mess that is genomics data.
-License: MIT
+Description: An extension of 'ggplot2' for creating complex genomic
+ maps. It builds on the power of 'ggplot2' and 'tidyverse' adding new 'ggplot2'-style
+ geoms & positions and 'dplyr'-style verbs to manipulate the underlying data. It
+ implements a layout concept inspired by 'ggraph' and introduces tracks to bring
+ tidiness to the mess that is genomics data.
+License: MIT + file LICENSE
 URL: https://github.com/thackl/gggenomes
 BugReports: https://github.com/thackl/gggenomes/issues
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.3.1
+Roxygen: list(markdown = TRUE)
+VignetteBuilder: knitr
 Depends:
     R (>= 3.4.2),
+    ggplot2 (>= 3.5.0),
+Imports:
+    vctrs,
+    rlang,
     dplyr,
-    ggplot2,
-    gggenes,
+    tidyr,
+    readr (>= 2.0.0),
     purrr,
-    readr,
+    tibble,
     stringr,
-    thacklr,
-    tibble
+    grid,
+    jsonlite,
+    snakecase,
+    magrittr,
+    scales,
+    tidyselect,
+    colorspace,
+    methods,
+    utils,
+    ellipsis
 Suggests:
     testthat,
-    rtracklayer
+    ggtree,
+    patchwork,
+    Hmisc,
+    knitr,
+    ggrepel,
+    IRanges,

LICENSE

@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2018 Thomas Hackl
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2018
+COPYRIGHT HOLDER: Thomas Hackl

LICENSE.md

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 Thomas Hackl
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.