Merge pull request #25 from m-jahn/dev

feat: various improvements for loading files, GH actions, linting, R CMD CHECK fixes

Author: m-jahn

.Rbuildignore

@@ -0,0 +1,13 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.github$
+^LICENSE\.md$
+^CODE_OF_CONDUCT\.md$
+^CONTRIBUTING\.md$
+^README\.Rmd$
+^cran-comments\.md$
+^CRAN-SUBMISSION$
+^_pkgdown\.yml$
+^docs$
+^vignettes/CustomizeThePlot\.Rmd$
+^vignettes/TimeAndMemory\.Rmd$

.github/workflows/R-CMD-check.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, dev]
+  pull_request:
+    branches: [main, dev]
+  workflow_dispatch:
+
+name: R-CMD-check
+
+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: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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

.gitignore

@@ -1,5 +1,4 @@
 inst/doc
 .Rhistory
-.Rbuildignore
 .Rproj*
 .Rproj.user

DESCRIPTION

@@ -1,20 +1,26 @@
 Package: ggcoverage
 Type: Package
 Title: Visualize Genome/Protein Coverage with Various Annotations
-Version: 1.2.0
-Authors@R: 
+Version: 1.3.0
+Authors@R: c(
     person(given = "Yabing",
            family = "Song",
            role = c("aut", "cre"),
-           email = "songyb0519@gmail.com")
+           email = "songyb0519@gmail.com"),
+    person(given = "Michael",
+           family = "Jahn", 
+           email = "jahn@mpusp.mpg.de",
+           role = "aut",
+           comment = c(ORCID = "0000-0002-3913-153X"))
+  )
 Maintainer: Yabing Song <songyb0519@gmail.com>
 Description: The goal of 'ggcoverage' is to simplify the process of visualizing genome/protein coverage. It contains functions to 
     load data from BAM, BigWig, BedGraph or txt/xlsx files, create genome/protein coverage plot, add various annotations to 
     the coverage plot, including base and amino acid annotation, GC annotation, gene annotation, transcript annotation, ideogram annotation,
     peak annotation, contact map annotation, link annotation and peotein feature annotation.
 License: MIT + file LICENSE
 Encoding: UTF-8
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 URL: https://showteeth.github.io/ggcoverage/, https://github.com/showteeth/ggcoverage
 BugReports: https://github.com/showteeth/ggcoverage/issues
 biocViews:
@@ -50,7 +56,7 @@ Imports:
     BiocParallel,
     openxlsx,
     stringr,
-    ggpp
+    gridExtra
 Suggests: 
     rmarkdown,
     knitr,

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2022
-COPYRIGHT HOLDER: ggtrack authors
+YEAR: 2022-2024
+COPYRIGHT HOLDER: ggcoverage authors

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2022 ggcoverage authors
+Copyright (c) 2022-2024 ggcoverage authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

NAMESPACE

@@ -73,11 +73,14 @@ importFrom(RColorBrewer,brewer.pal)
 importFrom(Rsamtools,ScanBamParam)
 importFrom(Rsamtools,indexBam)
 importFrom(S4Vectors,"values<-")
+importFrom(dplyr,all_of)
 importFrom(dplyr,arrange)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
+importFrom(dplyr,mutate)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
+importFrom(dplyr,summarize)
 importFrom(ggbio,layout_karyogram)
 importFrom(ggforce,geom_bezier)
 importFrom(ggh4x,elem_list_rect)
@@ -90,6 +93,7 @@ importFrom(ggplot2,aes_string)
 importFrom(ggplot2,annotate)
 importFrom(ggplot2,arrow)
 importFrom(ggplot2,coord_cartesian)
+importFrom(ggplot2,cut_width)
 importFrom(ggplot2,element_blank)
 importFrom(ggplot2,element_rect)
 importFrom(ggplot2,element_text)
@@ -118,10 +122,11 @@ importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_classic)
 importFrom(ggplot2,unit)
-importFrom(ggpp,annotate)
 importFrom(ggrepel,geom_text_repel)
 importFrom(grDevices,col2rgb)
 importFrom(grDevices,colorRampPalette)
+importFrom(gridExtra,tableGrob)
+importFrom(gridExtra,ttheme_default)
 importFrom(magrittr,"%>%")
 importFrom(methods,extends)
 importFrom(openxlsx,read.xlsx)

NEWS.md

@@ -1,3 +1,15 @@
+# ggcoverage 1.3.0
+## Major changes
+* Refactored `LoadTrack` function.
+* Added GH actions workflow to run automatic R CMD CHECK
+
+## Minor changes
+* Handle binning for bam files regardless if done via `bamCoverage` or `GenomicAlignments`.
+* Various small linting fixes.
+* Refactored `ggcoverage.Rmd` and `README.Rmd` in order to remove all lint errors, adhere to R code style
+
+-------------
+
 # ggcoverage 1.2.0
 ## Major changes
 * Support protein coverage and annotation plot (`ggprotein`, `geom_protein`, `geom_feature`).