BacArena: plotSpecActivity – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

plotSpecActivity

Function to plot substance usage for every species

Description

The generic function plotSpecActivity displays the input/output substances with the highest variance (could also be defiened manually) for all species

Usage

plotSpecActivity(
  simlist,
  subs = list(),
  var_nr = 10,
  spec_list = NULL,
  ret_data = FALSE,
  useNames = FALSE,
  rm_unused = TRUE,
  cutoff = 1e-06
)

Arguments

`simlist`	An object of class Eval or a list with objects of class Eval.
`subs`	List of substance names
`var_nr`	Number of most varying substances to be used (if subs is not specified)
`spec_list`	List of species names to be considered (default all)
`ret_data`	Set true if data should be returned
`useNames`	Use substance names instead of ids
`rm_unused`	Remove substances which do not change from plot
`cutoff`	Minimum valu for fluxes to be considered

Details

Returns ggplot objects

BacArena

Modeling Framework for Cellular Communities in their Environments

v1.8.2

GPL-3 | file LICENSE

Authors

Eugen Bauer [aut], Johannes Zimmermann [aut, cre]

Initial release