geom_coverage: Layer for Coverage Plot.

In ggcoverage: Visualize Genome Coverage with Various Annotations

Layer for Coverage Plot.

Description

Layer for Coverage Plot.

Usage

geom_coverage(
  data,
  mapping = NULL,
  color = NULL,
  rect.color = NA,
  facet.key = "Type",
  facet.order = NULL,
  facet.color = NULL,
  group.key = "Group",
  range.size = 3,
  range.position = c("in", "out"),
  mark.region = NULL,
  mark.color = "grey",
  mark.alpha = 0.5,
  show.mark.label = TRUE,
  mark.label.size = 4
)

Arguments

data	Track prepared by FormatTrack.
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.
facet.key	Sample type key to create coverage plot. Default: Type.
facet.order	The order of coverage plot. Default: NULL.
facet.color	The color of sample text. Default: NULL (select automatically).
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.
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

Layers of ggplot2.

Examples

library(ggcoverage)
library(utils)
library(ggplot2)
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
)
ggplot() +
  geom_coverage(data = track.df, color = "auto", mark.region = NULL)

ggcoverage documentation built on Sept. 6, 2022, 9:06 a.m.