Add Base and Amino Acid Annotation to Coverage Plot.

Add Base and Amino Acid Annotation to Coverage Plot.

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",
  mark.type = "twill",
  star.size = 1,
  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.border.color = "white",
  aa.size = 4,
  aa.margin = 2,
  aa.height = 0.4,
  plot.space = 2.5,
  plot.height = 0.5
)

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".
mark.type

The mark type to highlight SNV position, choose from twill (add twill to position with SNV), star (add star mark to position with SNV), and highlight (position without SNV is grey). Default: twill.
star.size

The size of star when mark.type is star. Default: 1.
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.border.color

The border color of amino acid. Default: white.
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.

Value

Plot.

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
#   )