Merge pull request #43 from m-jahn/dev

fix: reduced size footprint + examples for CRAN submission

Author: showteeth

DESCRIPTION

@@ -1,21 +1,21 @@
 Type: Package
 Package: ggcoverage
 Title: Visualize Genome/Protein Coverage with Various Annotations
-Version: 1.4.0
+Version: 1.4.1
 Authors@R: c(
     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 visualize coverage tracks from
+Description: The goal of 'ggcoverage' is to visualize coverage tracks from
     genomics, transcriptomics or proteomics data. It contains functions to
     load data from BAM, BigWig, BedGraph, txt, or xlsx files, create
     genome/protein coverage plots, and add various annotations including
     base and amino acid composition, GC content, copy number variation
     (CNV), genes, transcripts, ideograms, peak highlights, HiC contact
     maps, contact links and protein features. It is based on and
-    integrates well with `ggplot2`.
+    integrates well with 'ggplot2'.
 License: MIT + file LICENSE
 URL: https://showteeth.github.io/ggcoverage/,
     https://github.com/showteeth/ggcoverage
@@ -49,7 +49,6 @@ Suggests:
     ggforce,
     graphics,
     HiCBricks,
-    HiCDataHumanIMR90,
     htmltools,
     knitr,
     rmarkdown

R/geom_base.R

@@ -47,40 +47,41 @@
 #' @export
 #'
 #' @examples
-#' library("BSgenome.Hsapiens.UCSC.hg19")
+#' if (requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE)) {
+#'   library("BSgenome.Hsapiens.UCSC.hg19")
 #'
-#' # get sample metadata
-#' sample.meta <- data.frame(
-#'   SampleName = c("tumorA.chr4.selected"),
-#'   Type = c("tumorA"),
-#'   Group = c("tumorA")
-#' )
-#'
-#' # get bam file
-#' bam.file <-
-#'   system.file("extdata", "DNA-seq", "tumorA.chr4.selected.bam", package = "ggcoverage")
+#'   # get sample metadata
+#'   sample.meta <- data.frame(
+#'     SampleName = c("tumorA.chr4.selected"),
+#'     Type = c("tumorA"),
+#'     Group = c("tumorA")
+#'   )
 #'
-#' # load bam file
-#' track.df <- LoadTrackFile(
-#'   track.file = bam.file,
-#'   meta.info = sample.meta,
-#'   single.nuc = TRUE,
-#'   single.nuc.region = "chr4:62474235-62474295"
-#' )
+#'   # get bam file
+#'   bam.file <-
+#'     system.file("extdata", "DNA-seq", "tumorA.chr4.selected.bam", package = "ggcoverage")
 #'
-#' # plot
-#' ggcoverage(
-#'   data = track.df,
-#'   color = "grey",
-#'   range.position = "out",
-#'   single.nuc = TRUE,
-#'   rect.color = "white"
-#' ) +
-#'   geom_base(
-#'     bam.file = bam.file,
-#'     bs.fa.seq = BSgenome.Hsapiens.UCSC.hg19
+#'   # load bam file
+#'   track.df <- LoadTrackFile(
+#'     track.file = bam.file,
+#'     meta.info = sample.meta,
+#'     single.nuc = TRUE,
+#'     single.nuc.region = "chr4:62474235-62474295"
 #'   )
 #'
+#'   # plot
+#'   ggcoverage(
+#'     data = track.df,
+#'     color = "grey",
+#'     range.position = "out",
+#'     single.nuc = TRUE,
+#'     rect.color = "white"
+#'   ) +
+#'     geom_base(
+#'       bam.file = bam.file,
+#'       bs.fa.seq = BSgenome.Hsapiens.UCSC.hg19
+#'     )
+#' }
 geom_base <- function(bam.file, fa.file = NULL, bs.fa.seq = NULL, chr.split = "[[:space:]]",
                       nuc.offset = -0.1, nuc.size = 4, nuc.padding = 0.05, nuc.padding.r = 0,
                       nuc.color = c("A" = "#ff2b08", "C" = "#009aff", "G" = "#ffb507", "T" = "#00bc0d"),

R/geom_cnv.R

@@ -22,23 +22,36 @@
 #' @export
 #'
 #' @examples
-#' # library(ggcoverage)
-#' # library(utils)
-#' # library("BSgenome.Hsapiens.UCSC.hg19")
-#' # # prepare files
-#' # cnv.file <- system.file("extdata", "DNA-seq", "SRR054616_copynumber.txt", package = "ggcoverage")
-#' # track.file <- system.file("extdata", "DNA-seq", "SRR054616.bw", package = "ggcoverage")
-#' # # read CNV
-#' # cnv.df = read.table(file = cnv.file, sep = "\t", header = TRUE)
-#' # # load track
-#' # track.df = LoadTrackFile(track.file = track.file, format = "bw")
-#' # track.df$seqnames = paste0("chr", track.df$seqnames)
-#' # # plot
-#' # ggcoverage(data = track.df, color = "grey", region = "chr4:1-160000000",
-#' #            mark.region = NULL, range.position = "out") +
-#' #   geom_gc(bs.fa.seq=BSgenome.Hsapiens.UCSC.hg19) +
-#' #   geom_cnv(cnv.df = cnv.df, bin.col = 3, cn.col = 4) +
-#' #   geom_ideogram(genome = "hg19",plot.space = 0, highlight.centromere = TRUE)
+#' if (requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE)) {
+#'   library("BSgenome.Hsapiens.UCSC.hg19")
+#'
+#'   # load track data
+#'   track_file <-
+#'     system.file("extdata", "DNA-seq", "SRR054616.bw", package = "ggcoverage")
+#'   track_df <- LoadTrackFile(
+#'     track.file = track_file,
+#'     format = "bw",
+#'     region = "4:1-160000000"
+#'   )
+#'   track_df$seqnames <- paste0("chr", track_df$seqnames)
+#'
+#'   # read CNV data
+#'   cnv_file <-
+#'     system.file("extdata", "DNA-seq", "SRR054616_copynumber.txt", package = "ggcoverage")
+#'   cnv_df <- read.table(file = cnv_file, sep = "\t", header = TRUE)
+#'
+#'   # plot coverage, GC content, CNV
+#'   basic_coverage <- ggcoverage(
+#'     data = track_df,
+#'     color = "grey",
+#'     mark.region = NULL,
+#'     range.position = "out"
+#'   )
+#'
+#'   basic_coverage +
+#'     geom_gc(bs.fa.seq = BSgenome.Hsapiens.UCSC.hg19) +
+#'     geom_cnv(cnv.df = cnv_df, bin.col = 3, cn.col = 4)
+#' }
 geom_cnv <- function(cnv.df, bin.col = 3, cn.col = 4, ref.cn = 2,
                      bin.point.color = "grey", bin.point.alpha = 0.6, cn.line.color = "red",
                      ref.line.color = "black", plot.space = 0.1, plot.height = 0.2) {

R/geom_gc.R

@@ -20,20 +20,30 @@
 #' @export
 #'
 #' @examples
-#' # library(ggcoverage)
-#' # library(utils)
-#' # library(rtracklayer)
-#' # library("BSgenome.Hsapiens.UCSC.hg19")
-#' # track folder
-#' # track.file <- system.file("extdata", "DNA-seq", "CNV_example.txt", package = "ggcoverage")
-#' # track.df <- utils::read.table(track.file, header = TRUE)
-#' # gtf.file <- system.file("extdata", "used_hg19.gtf", package = "ggcoverage")
-#' # gtf.gr <- rtracklayer::import.gff(con = gtf.file, format = "gtf")
-#' # basic.coverage <- ggcoverage(
-#' #   data = track.df, color = NULL, mark.region = NULL,
-#' #   region = "chr4:61750000-62,700,000", range.position = "out"
-#' # )
-#' # basic.coverage + geom_gc(bs.fa.seq = BSgenome.Hsapiens.UCSC.hg19)
+#' if (requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE)) {
+#'   library("BSgenome.Hsapiens.UCSC.hg19")
+#'
+#'   # load track data
+#'   track_file <-
+#'     system.file("extdata", "DNA-seq", "SRR054616.bw", package = "ggcoverage")
+#'   track_df <- LoadTrackFile(
+#'     track.file = track_file,
+#'     format = "bw",
+#'     region = "4:1-160000000"
+#'   )
+#'   track_df$seqnames <- paste0("chr", track_df$seqnames)
+#'
+#'   # plot coverage and GC content
+#'   basic_coverage <- ggcoverage(
+#'     data = track_df,
+#'     color = "grey",
+#'     mark.region = NULL,
+#'     range.position = "out"
+#'   )
+#'
+#'   basic_coverage +
+#'     geom_gc(bs.fa.seq = BSgenome.Hsapiens.UCSC.hg19)
+#' }
 geom_gc <- function(fa.file = NULL, bs.fa.seq = NULL, chr.split = "[[:space:]]", guide.line = NULL,
                     line.color = "black", guide.line.color = "red", guide.line.type = "dashed",
                     plot.space = 0.1, plot.height = 0.2) {

R/geom_ideogram.R

@@ -36,6 +36,7 @@
 #'
 #' @examples
 #' \dontrun{
+#' # note that you need to have package 'ggbio' installed
 #' library(ggbio)
 #'
 #' # load metadata

R/geom_tad.R

@@ -23,53 +23,54 @@
 #' @importFrom utils write.table
 #'
 #' @examples
-#' library(ggcoverage)
-#' library(HiCBricks)
+#' if (requireNamespace("HiCBricks", quietly = TRUE)) {
+#'   library(HiCBricks)
 #'
-#' # prepare track dataframe
-#' track.file <- system.file("extdata", "HiC", "H3K36me3.bw", package = "ggcoverage")
-#' track.df <- LoadTrackFile(
-#'   track.file = track.file, format = "bw",
-#'   region = "chr2L:8050000-8300000", extend = 0
-#' )
-#' track.df$score <- ifelse(track.df$score < 0, 0, track.df$score)
-#' # check the data
-#' head(track.df)
+#'   # prepare track dataframe
+#'   track.file <- system.file("extdata", "HiC", "H3K36me3.bw", package = "ggcoverage")
+#'   track.df <- LoadTrackFile(
+#'     track.file = track.file, format = "bw",
+#'     region = "chr2L:8100000-8200000", extend = 0
+#'   )
+#'   track.df$score <- ifelse(track.df$score < 0, 0, track.df$score)
+#'   # check the data
+#'   head(track.df)
 #'
-#' # Load Hi-C data
-#' hic.mat.file <- system.file("extdata", "HiC", "HiC_mat.txt", package = "ggcoverage")
-#' hic.mat <- read.table(file = hic.mat.file, sep = "\t")
-#' hic.mat <- as.matrix(hic.mat)
+#'   # Load Hi-C data
+#'   hic.mat.file <- system.file("extdata", "HiC", "HiC_mat.txt", package = "ggcoverage")
+#'   hic.mat <- read.table(file = hic.mat.file, sep = "\t")
+#'   hic.mat <- as.matrix(hic.mat)
 #'
-#' # bin data
-#' hic.bin.file <- system.file("extdata", "HiC", "HiC_bin.txt", package = "ggcoverage")
-#' hic.bin <- read.table(file = hic.bin.file, sep = "\t")
-#' colnames(hic.bin) <- c("chr", "start", "end")
-#' hic.bin.gr <- GenomicRanges::makeGRangesFromDataFrame(df = hic.bin)
+#'   # bin data
+#'   hic.bin.file <- system.file("extdata", "HiC", "HiC_bin.txt", package = "ggcoverage")
+#'   hic.bin <- read.table(file = hic.bin.file, sep = "\t")
+#'   colnames(hic.bin) <- c("chr", "start", "end")
+#'   hic.bin.gr <- GenomicRanges::makeGRangesFromDataFrame(df = hic.bin)
 #'
-#' # transfrom function
-#' failsafe_log10 <- function(x) {
-#'   x[is.na(x) | is.nan(x) | is.infinite(x)] <- 0
-#'   return(log10(x + 1))
-#' }
+#'   # transfrom function
+#'   failsafe_log10 <- function(x) {
+#'     x[is.na(x) | is.nan(x) | is.infinite(x)] <- 0
+#'     return(log10(x + 1))
+#'   }
 #'
-#' # load link data: prepare arcs
-#' link.file <- system.file("extdata", "HiC", "HiC_link.bedpe", package = "ggcoverage")
+#'   # load link data: prepare arcs
+#'   link.file <- system.file("extdata", "HiC", "HiC_link.bedpe", package = "ggcoverage")
 #'
-#' # basic coverage
-#' basic.coverage <- ggcoverage(
-#'   data = track.df, color = "grey",
-#'   mark.region = NULL, range.position = "out"
-#' )
+#'   # basic coverage
+#'   basic.coverage <- ggcoverage(
+#'     data = track.df, color = "grey",
+#'     mark.region = NULL, range.position = "out"
+#'   )
 #'
-#' # add annotations
-#' basic.coverage +
-#'   geom_tad(
-#'     matrix = hic.mat, granges = hic.bin.gr, value.cut = 0.99,
-#'     color.palette = "viridis", transform.fun = failsafe_log10,
-#'     top = FALSE, show.rect = TRUE
-#'   ) +
-#'   geom_link(link.file = link.file, file.type = "bedpe", show.rect = TRUE)
+#'   # add annotations
+#'   basic.coverage +
+#'     geom_tad(
+#'       matrix = hic.mat, granges = hic.bin.gr, value.cut = 0.99,
+#'       color.palette = "viridis", transform.fun = failsafe_log10,
+#'       top = FALSE, show.rect = TRUE
+#'     ) +
+#'     geom_link(link.file = link.file, file.type = "bedpe", show.rect = TRUE)
+#' }
 #'
 #' @export
 geom_tad <- function(matrix, granges, color.palette = NULL, value.cut = NULL,

R/geom_transcript.R

@@ -46,10 +46,6 @@
 #' @export
 #'
 #' @examples
-#' library(ggcoverage)
-#' library(utils)
-#' library(rtracklayer)
-#'
 #' # load metadata
 #' meta_file <- system.file("extdata", "RNA-seq", "meta_info.csv", package = "ggcoverage")
 #' sample_meta <- read.csv(meta_file)
@@ -75,20 +71,6 @@
 #' basic_coverage +
 #'   geom_transcript(gtf.gr = gtf_gr, label.vjust = 1.5)
 #'
-#' # plot with custom style
-#' basic_coverage +
-#'   geom_transcript(
-#'     gtf.gr = gtf_gr,
-#'     exon.size = 2.0,
-#'     arrow.size.im = 1.0,
-#'     arrow.length.im = 5,
-#'     arrow.type.im = "open",
-#'     color.by.im = "strand",
-#'     fill.color = c(
-#'       "-" = "darkblue",
-#'       "+" = "darkgreen"
-#'     )
-#'   )
 geom_transcript <-
   function(gtf.gr,
            gene.name = "HNRNPC",

README.Rmd

@@ -317,7 +317,9 @@ basic_coverage
 
 ##### Add GC annotations
 
-Add **GC**, **ideogram** and **gene** annotaions.
+Add **GC**, **ideogram** and **gene** annotations.
+The plotting of the GC content requires the genome annotation package `BSgenome.Hsapiens.UCSC.hg19`.
+This package needs to be installed separately (it is only 'Suggested' by `ggcoverage`).
 
 ```{r gc_coverage, warning = FALSE, fig.height = 10, fig.width = 12, fig.align = "center"}
 # load genome data

README.md

@@ -423,7 +423,10 @@ basic_coverage
 
 ##### Add GC annotations
 
-Add **GC**, **ideogram** and **gene** annotaions.
+Add **GC**, **ideogram** and **gene** annotations. The plotting of the
+GC content requires the genome annotation package
+`BSgenome.Hsapiens.UCSC.hg19`. This package needs to be installed
+separately (it is only ‘Suggested’ by `ggcoverage`).
 
 ``` r
 # load genome data
@@ -657,7 +660,7 @@ graphics::par(opar)
 
 Default color scheme for amino acid annotation is from [Residual
 colours: a proposal for
-aminochromography](https://doi.org/10.1093/protein/10.7.743):
+aminochromography](https://pubmed.ncbi.nlm.nih.gov/9342138/):
 
 ``` r
 aa_color <- c(
@@ -898,7 +901,7 @@ a contact map.
 
 The Hi-C data is taken from [pyGenomeTracks: reproducible plots for
 multivariate genomic
-datasets](https://doi.org/10.1093/bioinformatics/btaa692).
+datasets](https://pubmed.ncbi.nlm.nih.gov/32745185/).
 
 The Hi-C matrix visualization is implemented by
 [`HiCBricks`](https://github.com/koustav-pal/HiCBricks). This package