Merge pull request #31 from m-jahn/dev

feat: various improvements for CRAN release version 1.4.0

Author: m-jahn

.gitignore

@@ -2,3 +2,5 @@ inst/doc
 .Rhistory
 .Rproj*
 .Rproj.user
+vignettes/*.html
+vignettes/png/*

DESCRIPTION

@@ -1,68 +1,60 @@
-Package: ggcoverage
 Type: Package
+Package: ggcoverage
 Title: Visualize Genome/Protein Coverage with Various Annotations
-Version: 1.3.0
+Version: 1.4.0
 Authors@R: c(
-    person(given = "Yabing",
-           family = "Song",
-           role = c("aut", "cre"),
-           email = "[email protected]"),
-    person(given = "Michael",
-           family = "Jahn", 
-           email = "[email protected]",
-           role = "aut",
+    person("Yabing", "Song", , "[email protected]", role = c("aut", "cre", "cph")),
+    person("Michael", "Jahn", , "[email protected]", role = c("aut", "cph"),
            comment = c(ORCID = "0000-0002-3913-153X"))
   )
-Maintainer: Yabing Song <[email protected]>
-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.
+Maintainer: Michael Jahn <[email protected]>
+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 plots, 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 protein
+    feature annotation.
 License: MIT + file LICENSE
-Encoding: UTF-8
-RoxygenNote: 7.3.1
-URL: https://showteeth.github.io/ggcoverage/, https://github.com/showteeth/ggcoverage
+URL: https://showteeth.github.io/ggcoverage/,
+    https://github.com/showteeth/ggcoverage
 BugReports: https://github.com/showteeth/ggcoverage/issues
-biocViews:
 Imports: 
+    BiocParallel,
+    Biostrings,
     dplyr,
+    GenomeInfoDb,
+    GenomicAlignments,
     GenomicRanges,
-    ggbio,
     ggh4x,
+    ggpattern,
     ggplot2,
     ggrepel,
     grDevices,
+    gridExtra,
     IRanges,
-    magrittr,
+    methods,
     patchwork,
-    RColorBrewer,
     rlang,
     Rsamtools,
     rtracklayer,
     scales,
     stats,
-    utils,
-    methods,
-    GenomeInfoDb,
-    S4Vectors,
-    Biostrings,
-    BSgenome,
-    GenomicAlignments,
-    reshape2,
-    seqinr,
-    ggforce,
-    HiCBricks,
-    ggpattern,
-    BiocParallel,
-    openxlsx,
-    stringr,
-    gridExtra
+    utils
 Suggests: 
-    rmarkdown,
-    knitr,
     BiocStyle,
-    htmltools,
     BSgenome.Hsapiens.UCSC.hg19,
+    ggbio,
+    ggforce,
     graphics,
-    HiCDataHumanIMR90
-VignetteBuilder: knitr
+    HiCBricks,
+    HiCDataHumanIMR90,
+    htmltools,
+    knitr,
+    rmarkdown
+VignetteBuilder: 
+    knitr
+biocViews:
+Encoding: UTF-8
+RoxygenNote: 7.3.1

NAMESPACE

@@ -14,6 +14,7 @@ export(FormatTrack)
 export(GetConsensusPeak)
 export(GetPlotData)
 export(LoadTrackFile)
+export(geom_arrows)
 export(geom_base)
 export(geom_cnv)
 export(geom_coverage)
@@ -45,14 +46,14 @@ export(theme_protein2)
 export(theme_tad)
 export(theme_tad2)
 export(theme_transcript)
-import(HiCBricks)
-importFrom(BSgenome,getSeq)
 importFrom(BiocParallel,MulticoreParam)
 importFrom(BiocParallel,bplapply)
 importFrom(BiocParallel,register)
+importFrom(Biostrings,getSeq)
 importFrom(Biostrings,letterFrequency)
 importFrom(Biostrings,readAAStringSet)
 importFrom(Biostrings,readDNAStringSet)
+importFrom(Biostrings,translate)
 importFrom(GenomeInfoDb,"seqlengths<-")
 importFrom(GenomeInfoDb,seqlengths)
 importFrom(GenomeInfoDb,seqnames)
@@ -69,10 +70,9 @@ importFrom(GenomicRanges,trim)
 importFrom(IRanges,IRanges)
 importFrom(IRanges,findOverlaps)
 importFrom(IRanges,subsetByOverlaps)
-importFrom(RColorBrewer,brewer.pal)
 importFrom(Rsamtools,ScanBamParam)
 importFrom(Rsamtools,indexBam)
-importFrom(S4Vectors,"values<-")
+importFrom(dplyr,"%>%")
 importFrom(dplyr,all_of)
 importFrom(dplyr,arrange)
 importFrom(dplyr,filter)
@@ -81,8 +81,6 @@ 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)
 importFrom(ggh4x,facet_wrap2)
 importFrom(ggh4x,strip_themed)
@@ -99,6 +97,7 @@ importFrom(ggplot2,element_rect)
 importFrom(ggplot2,element_text)
 importFrom(ggplot2,expansion)
 importFrom(ggplot2,geom_bar)
+importFrom(ggplot2,geom_curve)
 importFrom(ggplot2,geom_hline)
 importFrom(ggplot2,geom_label)
 importFrom(ggplot2,geom_line)
@@ -114,7 +113,7 @@ importFrom(ggplot2,ggplot_add)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,margin)
 importFrom(ggplot2,rel)
-importFrom(ggplot2,scale_color_gradient2)
+importFrom(ggplot2,scale_color_gradientn)
 importFrom(ggplot2,scale_color_manual)
 importFrom(ggplot2,scale_fill_manual)
 importFrom(ggplot2,scale_x_continuous)
@@ -125,22 +124,25 @@ importFrom(ggplot2,unit)
 importFrom(ggrepel,geom_text_repel)
 importFrom(grDevices,col2rgb)
 importFrom(grDevices,colorRampPalette)
+importFrom(grDevices,grey)
 importFrom(gridExtra,tableGrob)
 importFrom(gridExtra,ttheme_default)
-importFrom(magrittr,"%>%")
 importFrom(methods,extends)
-importFrom(openxlsx,read.xlsx)
 importFrom(patchwork,wrap_plots)
-importFrom(reshape2,melt)
 importFrom(rlang,.data)
 importFrom(rlang,as_label)
+importFrom(rtracklayer,GRangesForUCSCGenome)
+importFrom(rtracklayer,browserSession)
+importFrom(rtracklayer,getTable)
 importFrom(rtracklayer,import)
+importFrom(rtracklayer,tableName)
+importFrom(rtracklayer,ucscGenomes)
+importFrom(rtracklayer,ucscTableQuery)
 importFrom(scales,comma)
 importFrom(scales,rescale)
 importFrom(scales,scientific)
-importFrom(seqinr,translate)
 importFrom(stats,as.formula)
-importFrom(stringr,str_locate)
+importFrom(stats,reshape)
 importFrom(utils,menu)
 importFrom(utils,read.csv)
 importFrom(utils,read.table)

NEWS.md

@@ -1,3 +1,15 @@
+# ggcoverage 1.4.0
+## Major changes
+* removed 11 strict dependencies, refactored many functions to work with basic solutions
+* formatted all R code with 'styler'
+* improved arrow style for genomic features
+
+## Minor changes
+* fixed overlapping gene arrows issue
+* dont run failing ideogram example check
+* fixed unavailable URLS
+* use tidy description
+
 # ggcoverage 1.3.0
 ## Major changes
 * Refactored `LoadTrack` function.

R/ConsensusPeak.R

@@ -26,7 +26,6 @@
 GetConsensusPeak <- function(peak.file, peak.folder = NULL, mspc.path = NULL, rep.type = c("bio", "tec"), stringency.threshold = 1e-8,
                              weak.threshold = 1e-4, gamma = 1e-8, alpha = 0.05, min.overlap.num = 1,
                              multiple.intersections = c("Lowest", "Highest"), parallelism.degree = 1) {
-
   # check parameters
   rep.type <- match.arg(arg = rep.type)
   multiple.intersections <- match.arg(arg = multiple.intersections)

R/FormatInput.R

@@ -41,7 +41,7 @@ GetRegion <- function(df, chr, start, end = NULL) {
 #' @param extend Extend length of \code{region}. Default: 2000.
 #'
 #' @return A dataframe.
-#' @importFrom magrittr %>%
+#' @importFrom dplyr %>%
 #' @importFrom dplyr filter arrange
 #'
 #' @export

R/LoadTrack.R

@@ -31,7 +31,7 @@
 #' @importFrom GenomicAlignments alphabetFrequencyFromBam readGAlignments coverage
 #' @importFrom GenomicRanges GRanges
 #' @importFrom IRanges IRanges subsetByOverlaps
-#' @importFrom magrittr %>%
+#' @importFrom dplyr %>%
 #' @importFrom dplyr select filter mutate all_of group_by summarize
 #' @importFrom BiocParallel register MulticoreParam bplapply
 #' @importFrom ggplot2 cut_width
@@ -56,17 +56,16 @@
 #'   meta.info = sample.meta
 #' )
 LoadTrackFile <- function(
-  track.file, track.folder = NULL,
-  format = c("bam", "wig", "bw", "bedgraph", "txt"),
-  region = NULL, extend = 2000,
-  gtf.gr = NULL, gene.name = "HNRNPC",
-  gene.name.type = c("gene_name", "gene_id"),
-  meta.info = NULL, meta.file = "",
-  bamcoverage.path = NULL,
-  norm.method = c("RPKM", "CPM", "BPM", "RPGC", "None"),
-  single.nuc = FALSE, single.nuc.region = NULL,
-  bin.size = 10, bc.extra.para = NULL, n.cores = 1
-) {
+    track.file, track.folder = NULL,
+    format = c("bam", "wig", "bw", "bedgraph", "txt"),
+    region = NULL, extend = 2000,
+    gtf.gr = NULL, gene.name = "HNRNPC",
+    gene.name.type = c("gene_name", "gene_id"),
+    meta.info = NULL, meta.file = "",
+    bamcoverage.path = NULL,
+    norm.method = c("RPKM", "CPM", "BPM", "RPGC", "None"),
+    single.nuc = FALSE, single.nuc.region = NULL,
+    bin.size = 10, bc.extra.para = NULL, n.cores = 1) {
   # check parameters
   format <- match.arg(arg = format)
   gene.name.type <- match.arg(arg = gene.name.type)
@@ -83,8 +82,8 @@ LoadTrackFile <- function(
     if (format == "bam") {
       seqnames <- Rsamtools::scanBamHeader(track.file[1]) %>%
         lapply(function(x) x$targets) %>%
-        unname %>%
-        unlist
+        unname() %>%
+        unlist()
       gr <- GenomicRanges::GRanges(
         seqnames = names(seqnames[1]),
         IRanges(start = 1, end = min(100000, seqnames[1]))
@@ -128,20 +127,20 @@ LoadTrackFile <- function(
       BiocParallel::bplapply(track.file, BPPARAM = BiocParallel::MulticoreParam(), FUN = index_bam)
     }
     if (single.nuc) {
-        if (is.null(n.cores) || n.cores == 1) {
-          track.list <- lapply(
-            track.file,
-            single_nuc_cov,
-            single.nuc.region
-          )
-        } else {
-          track.list <- BiocParallel::bplapply(
-            track.file,
-            BPPARAM = BiocParallel::MulticoreParam(),
-            FUN = single_nuc_cov,
-            single.nuc.region
-          )
-        }
+      if (is.null(n.cores) || n.cores == 1) {
+        track.list <- lapply(
+          track.file,
+          single_nuc_cov,
+          single.nuc.region
+        )
+      } else {
+        track.list <- BiocParallel::bplapply(
+          track.file,
+          BPPARAM = BiocParallel::MulticoreParam(),
+          FUN = single_nuc_cov,
+          single.nuc.region
+        )
+      }
     } else {
       if (norm.method == "None") {
         message("Calculating coverage with GenomicAlignments when 'norm.method = None'")
@@ -310,8 +309,7 @@ single_nuc_cov <- function(x, single.nuc.region) {
 }
 
 bam_coverage <- function(
-  x, bamcoverage.path, bin.size, norm.method, bc.extra.para, gr
-) {
+    x, bamcoverage.path, bin.size, norm.method, bc.extra.para, gr) {
   # bigwig file
   out.bw.file <- tempfile(fileext = c(".bw"))
   # prepare bamCoverage cmd