fix: included tests for optional packages; reduced run time

Author: m-jahn

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