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Create a metabolic map with fluxes and export as SVG file

Source: R/map_visualization.R
flux_to_map.Rd

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.