Add Transcript Annotation to Coverage Plot.

geom_transcript(
  gtf.gr,
  gene.name = "HNRNPC",
  overlap.tx.gap = 0.1,
  overlap.style = "loose",
  tx.size = 1,
  utr.size = 2,
  exon.size = 4,
  arrow.size = 1,
  color.by = "strand",
  fill.color = c(`-` = "darkblue", `+` = "darkgreen"),
  arrow.gap = NULL,
  arrow.num = 50,
  arrow.length = 0.06,
  label.size = 3,
  label.vjust = 2,
  plot.space = 0.1,
  plot.height = 1
)

Arguments

gtf.gr	Granges object of GTF, created with `import.gff`. Default: NULL.
gene.name	Gene name of all transcripts. Default: HNRNPC.
overlap.tx.gap	The gap between transcript groups. Default: 0.1.
overlap.style	The style of transcript groups, choose from loose (each transcript occupies single line) and tight (place non-overlap transcripts in one line). Default: loose.
tx.size	The line size of transcript. Default: 1.
utr.size	The line size of UTR. Default: 2.
exon.size	The line size of exon. Default: 4.
arrow.size	The line size of arrow. Default: 1.
color.by	Color the line by. Default: strand.
fill.color	Color used for `color.by`. Default: darkblue for - (minus strand), darkgreen for + (plus strand).
arrow.gap	The gap distance between arrow. Default: NULL.
arrow.num	Total arrow num of whole region. Default: 50.
arrow.length	The length of arrow. Default: 0.06.
label.size	The size of transcript label. Default: 3.
label.vjust	The vjust of transcript label. Default: 2.
plot.space	Top and bottom margin. Default: 0.1.
plot.height	The relative height of transcript annotation to coverage plot. Default: 0.2.

Value

Plot.

Examples

# library(ggcoverage)
# library(utils)
# library(rtracklayer)
# meta.file <- system.file("extdata", "RNA-seq", "meta_info.csv", package = "ggcoverage")
# sample.meta <- utils::read.csv(meta.file)
# track folder
# track.folder <- system.file("extdata", "RNA-seq", package = "ggcoverage")
# load bigwig file
# track.df <- LoadTrackFile(
#   track.folder = track.folder, format = "bw",
#   meta.info = sample.meta
# )
# 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 = "auto", range.position = "out")
# basic.coverage + geom_transcript(gtf.gr = gtf.gr, label.vjust = 1.5)