plot_fragments: Plot all fragments for a given UniProt accession
In evanamartin/TopPICR: What the Package Does (One Line, Title Case)

plot_fragments

R Documentation

Plot all fragments for a given UniProt accession

Description

Plots all fragments associated with a given accession. If a gene name is provided a separate plot will be produced for each accession within the specified gene.

Usage

plot_fragments(
  x,
  gene = NULL,
  accession = NULL,
  turbo = TRUE,
  viridis = NULL,
  size = 1,
  color = "white",
  save_plot = FALSE,
  file_path = NULL
)

Arguments

`x`	A `data.table` output from the `create_mdata` function.
`gene`	A character string. A plot will be produced for each UniProt accession mapping to the specified gene. When a `gene` is specified `accession` does not also need to be specified.
`accession`	A character string specifying which UniProt accession will be plotted.
`turbo`	A logical value indicating whether the Turbo colormap will be used.
`viridis`	A character string indicating which colormap option will be used. The available options are: "magma" (or "A"), "inferno" (or "B"), "plasma" (or "C"), "viridis" (or "D") and "cividis" (or "E").
`size`	An integer specifying the size of the border around each fragment. The default size is 1.
`color`	A character string indicating the color of the border around each fragment. The default is white.
`save_plot`	A logical value. If TRUE the plot will be saved as a PNG file. When a plot is saved to a file it is not also displayed in R/RStudio.
`file_path`	The path to the folder where each plot will be saved. This must be specified if `save_plot` is TRUE.