ggcoverage (version 0.7.1)

geom_base: Add Base and Amino Acid Annotation to Coverage Plot.

Description

Add Base and Amino Acid Annotation to Coverage Plot.

Usage

geom_base(
  bam.file,
  fa.file = NULL,
  bs.fa.seq = NULL,
  chr.split = "[[:space:]]",
  nuc.offset = -0.1,
  nuc.size = 4,
  nuc.padding = 0.05,
  nuc.padding.r = 0,
  nuc.color = c(A = "#ff2b08", C = "#009aff", G = "#ffb507", T = "#00bc0d"),
  guide.line = NULL,
  guide.line.color = "red",
  guide.line.type = "dashed",
  show.aa = TRUE,
  sens = "F",
  numcode = 1,
  NAstring = "X",
  ambiguous = FALSE,
  aa.color = c(D = "#FF0000", S = "#FF2400", T = "#E34234", G = "#FF8000", P =
    "#F28500", C = "#FFFF00", A = "#FDFF00", V = "#E3FF00", I = "#C0FF00", L = "#89318C",
    M = "#00FF00", F = "#50C878", Y = "#30D5C8", W = "#00FFFF", H = "#0F2CB3", R =
    "#0000FF", K = "#4b0082", N = "#800080", Q = "#FF00FF", E = "#8F00FF", `*` =
    "#FFC0CB"),
  aa.size = 4,
  aa.margin = 2,
  aa.height = 0.4,
  plot.space = 2.5,
  plot.height = 0.5
)

Value

Plot.

Arguments

bam.file

BAM file.

fa.file

Genome fasta file. Default: NULL.

bs.fa.seq

BSgenome for species. Default: NULL.

chr.split

Split between chromosome name and description in fa.file. Default: "[[:space:]]".

nuc.offset

Offset of nucleotide to frequency plot. Default: -0.1.

nuc.size

The size of nucleotide text. Default: 4.

nuc.padding

Background padding of nucleotide annotation. Default: 0.05.

nuc.padding.r

Radius of background padding. Default: 0.

nuc.color

Color scheme for nucleotides. Default: "A": "#ff2b08", "C": "#009aff", "G": "#ffb507", "T": "#00bc0d".

guide.line

Nucleotide frequency guide line. Default: NULL (0.5).

guide.line.color

The color of guide line. Default: "red".

guide.line.type

The line type of guide line. Default: "dashed".

show.aa

Logical value, whether to show amino acid. Default: TRUE.

sens

Sense to translate: F for forward sense and R for reverse sense. Parameter of translate. Default: F.

numcode

The ncbi genetic code number for translation. Parameter of translate. By default the standard genetic code is used.

NAstring

How to translate amino-acids when there are ambiguous bases in codons. Parameter of translate. Default: X.

ambiguous

If TRUE, ambiguous bases are taken into account so that for instance GGN is translated to Gly in the standard genetic code. Parameter of translate. Default: FALSE.

aa.color

Color scheme for amino acids.

aa.size

The size of amino acid text. Default: 4.

aa.margin

Top and bottom margin of amino acids. Default: 2.

aa.height

The relative height of amino acid to base frequency plot. Default: 0.4.

plot.space

Top and bottom margin. Default: 2.5.

plot.height

The relative height of base and amino acid annotation to coverage plot. Default: 0.5.

Examples

library(ggcoverage)
library("BSgenome.Hsapiens.UCSC.hg19")
# get sample metadata
sample.meta <- data.frame(
  SampleName = c("tumorA.chr4.selected"),
  Type = c("tumorA"), Group = c("tumorA")
)
# get bam file
bam.file <- system.file("extdata", "DNA-seq", "tumorA.chr4.selected.bam", package = "ggcoverage")
# load bam file
track.df <- LoadTrackFile(
  track.file = bam.file,
  meta.info = sample.meta, single.nuc = TRUE,
  single.nuc.region = "chr4:62474235-62474295"
)
ggcoverage(
  data = track.df, color = "grey", range.position = "out",
  single.nuc = TRUE, rect.color = "white"
) +
  geom_base(
    bam.file = bam.file,
    bs.fa.seq = BSgenome.Hsapiens.UCSC.hg19
  )