ggcoverage: Create Coverage Plot.

In ggcoverage: Visualize Genome Coverage with Various Annotations

Create Coverage Plot.

Description

Create Coverage Plot.

Usage

ggcoverage(
  data,
  region = "chr14:21,677,306-21,737,601",
  gtf.gr = NULL,
  extend = 2000,
  gene.name = "HNRNPC",
  gene.name.type = c("gene_name", "gene_id"),
  single.nuc = FALSE,
  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"),
  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.
region	Region used to create coverage plot, eg: chr14:21,677,306-21,737,601 or chr14:21,677,306. Default: NULL.
gtf.gr	Granges object of GTF, created with import.gff. Default: NULL.
extend	Extend length of region. Default: 2000.
gene.name	The name of gene. Default: HNRNPC.
gene.name.type	Gene name type (filed of gtf.gr), chosen from gene_name and gene_id. Default: gene_name.
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.
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.
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",
  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")

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