plotSpecActivity: Function to plot substance usage for every species

In euba/BacArena: Modeling Framework for Cellular Communities in their Environments

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

euba/BacArena documentation built on March 27, 2024, 2:33 p.m.