flux_to_map: Create a metabolic map with fluxes and export as SVG file

In NicWir/VisomX: User-Friendly and Comprehensive Analysis and Visualization of Omics Data

Create a metabolic map with fluxes and export as SVG file

Description

flux_to_map takes a table file or dataframe as well as a template map in SVG format to visualize metabolic flux values in their metabolic context.

Usage

flux_to_map(
  df,
  template = NULL,
  result.nm = NULL,
  pal = c("G", "R", "O", "B", "BYR", "BW", "YR", "PuRd"),
  title = "",
  export = TRUE,
  inkscape_path = "C:/Program Files/Inkscape/bin/inkscape.exe",
  export_dpi = 300,
  export_width = 2281,
  export_height = 2166,
  FBA = FALSE
)

Arguments

df	A dataframe containing fluxes and standard deviations.
template	A template SVG file containing the metabolic map.
result.nm	The name of the output SVG file.
pal	The color palette for the flux arrows. G, green; R, red; O, orange; BYR, blue-yellow-red; BW, black-white (grayscale); YR, yellow-red; PuRd, purple-red.
title	The title of the output plot.
export	A logical value indicating whether to export the plot as a PNG and PDF file.
inkscape_path	The local path to the 'inkscape.exe' file. Required if export = TRUE.
export_dpi	The dpi of the exported PNG and PDF file.
export_width	The width of the exported PNG and PDF file. The width of the template SVG can be inspected after opening it in InkScape.
export_height	The height of the exported PNG and PDF file. The height of the template SVG can be inspected after opening it in InkScape.
FBA	A logical value indicating whether the dataframe contains FBA results. If TRUE, standard deviations are ignored.

Value

A metabolic map with fluxes.

NicWir/VisomX documentation built on Dec. 8, 2024, 1:27 a.m.