networkDFfromMPoutput {microPop}

networkDFfromMPoutput

Description

make node and edge data frames from microPop output to use in visNetwork

Usage

networkDFfromMPoutput(
  chosen.time,
  MPoutput,
  groupNames = NULL,
  sumOverPaths = TRUE,
  sumOverStrains = TRUE,
  convertToMoles = TRUE
)

Arguments

chosen.time

the time you want to plot

MPoutput

the output from microPopModel()

groupNames

Default is NULL which plots all the microbes. To plot a subset of all the groups, specify a vector of strings of the names of the groups you want to plot.

sumOverPaths

Logical. Default is TRUE which sums flows between the same nodes even if they are on different metabolic paths

sumOverStrains

Logical. Default is TRUE which means the strains are put into their functional group nodes and the flow are summed. When it is FALSE, each strain will have its own node.

convertToMoles

Logical. Default is TRUE

Value

a list containing the edges and nodes