ggcoverage (version 0.7.1)

geom_coverage: 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
)

Value

Layers of ggplot2.

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.

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)