Layer for Protein Coverage Plot.

Layer for Protein Coverage Plot.

geom_protein(
  coverage.file,
  fasta.file,
  protein.id,
  XCorr.threshold = 2,
  confidence = "High",
  contaminant = NULL,
  remove.na = TRUE,
  color = "grey",
  mark.bare = TRUE,
  mark.color = "red",
  mark.alpha = 0.5,
  show.table = TRUE,
  table.position = c("right_top", "left_top", "left_bottom", "right_bottom"),
  table.size = 4,
  table.color = "black",
  range.size = 3,
  range.position = c("in", "out")
)

Arguments

coverage.file

Exported protein coverage file, should be in excel.
fasta.file

Input reference protein fasta file.
protein.id

The protein ID of exported coverage file. This should be unique and in fasta.file.
XCorr.threshold

The cross-correlation threshold. Default: 2.
confidence

The confidence level. Default: High.
contaminant

Whether to remove contaminant peptides. Default: NULL (not remove).
remove.na

Logical value, whether to remove NA value in Abundance column. Default: TRUE.
color

The fill color of coverage plot. Default: grey.
mark.bare

Logical value, whether to mark region where Abundance is zero or NA. Default: TRUE.
mark.color

The color used for the marked region. Default: red.
mark.alpha

The transparency used for the marked region. Default: 0.5.
show.table

Logical value, whether to show coverage summary table. Default: TRUE.
table.position

The position of the coverage summary table, choose from right_top, left_top, left_bottom, right_bottom. Default: right_top.
table.size

The font size of coverage summary table. Default: 4.
table.color

The font color of coverage summary table. Default: black.
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.

Value

A ggplot2 object.

Examples

# library(ggplot2)
# library(ggcoverage)
# coverage.file <- system.file("extdata", "Proteomics", "MS_BSA_coverage.xlsx", package = "ggcoverage")
# fasta.file <- system.file("extdata", "Proteomics", "MS_BSA_coverage.fasta", package = "ggcoverage")
# protein.id = "sp|
# ggplot() +
#     geom_peptide(coverage.file = coverage.file, fasta.file = fasta.file, protein.id = protein.id)