Create Coverage Plot.

Create Coverage Plot.

ggcoverage(
  data,
  single.nuc = FALSE,
  mapping = NULL,
  color = NULL,
  rect.color = NA,
  plot.type = c("facet", "joint"),
  facet.key = "Type",
  joint.avg = FALSE,
  facet.order = NULL,
  facet.color = NULL,
  facet.y.scale = c("free", "fixed"),
  group.key = "Group",
  range.size = 3,
  range.position = c("in", "out"),
  plot.space = 0.2,
  mark.region = NULL,
  mark.color = "grey",
  mark.alpha = 0.5,
  show.mark.label = TRUE,
  mark.label.size = 4
)

Arguments

data

Coverage dataframe loaded by LoadTrackFile.
single.nuc

Logical value, whether to visualize at single nucleotide level. Default: FALSE.
mapping

Set of aesthetic mappings created by aes or aes_. Default: NULL.
color

Track color. Default: NULL (select automatically).
rect.color

The color of every bin. Default: NA.
plot.type

The type of the plot, choose from facet (separate plot for every sample) and joint (combine all sample in a single plot). Default: facet.
facet.key

Sample type key to create coverage plot. Default: Type.
joint.avg

Logical value, whether to show average coverage across group.key. Default: FALSE.
facet.order

The order of Coverage plot. Default: NULL.
facet.color

The color of sample text. Default: NULL (select automatically).
facet.y.scale

The shared type of y-axis scales across facets, choose from free (facets have different y-axis scales), fixed (facets have same y-axis scales). Default: free.
group.key

Group of samples. Default: NULL.
range.size

The label size of range text, used when range.position is in. Default: 3.
range.position

The position of y axis range, chosen from in (move y axis in the plot) and out (normal y axis). Default: in.
plot.space

The space between every facet. Default: 0.2.
mark.region

Mark region on the plot. Default: NULL.
mark.color

The color of marked region. Default: "grey".
mark.alpha

The alpha of marked region. Default: 0.5.
show.mark.label

Logical value, whether to show mark label (use label column in mark.region). Default: TRUE.
mark.label.size

The label size of mark label. Default: 4.

Value

A ggplot2 object.

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",region = "chr14:21,677,306-21,737,601",
#                           extend = 2000, meta.info = sample.meta)
# gtf.file <- system.file("extdata", "used_hg19.gtf", package = "ggcoverage")
# gtf.gr <- rtracklayer::import.gff(con = gtf.file, format = "gtf")
# ggcoverage(data = track.df, color = "auto", range.position = "out")