Nothing
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
## ----results='hide'-----------------------------------------------------------
library(microPop)
library(visNetwork)
## -----------------------------------------------------------------------------
v1=networkDFfromMPinput('Bacteroides') #this produces the network nodes and edges dataframes (contained in the list v1)
v2=getVNPlotObject(v1$nodes,v1$edges) #this takes the nodes and edges and makes the visNetwork object for plotting
visOptions(v2) #this produces a plot of the network. You can also use print(v2)
## -----------------------------------------------------------------------------
data(package='microPop')
## -----------------------------------------------------------------------------
microbes=c('Acetogens','ButyrateProducers1','Bacteroides','Methanogens')
DFs=networkDFfromMPinput(microbes)
nodes=DFs$nodes
edges=DFs$edges
vv=getVNPlotObject(nodes,edges,
addLegend=TRUE,
figWidth=600,
figHeight=600)
visOptions(vv)
## -----------------------------------------------------------------------------
vv=getVNPlotObject(nodes,edges,
addLegend=TRUE,
microbeCol='pink',
resourceCol='cyan',
productionCol='red',
uptakeCol='purple',
figWidth=600,
figHeight=600)
visOptions(vv)
## -----------------------------------------------------------------------------
allMicrobes=c('Acetogens','ButyrateProducers1','ButyrateProducers2','ButyrateProducers3',
'Bacteroides','Methanogens','LactateProducers',
'NoButyFibreDeg','NoButyStarchDeg','PropionateProducers')
DFs=networkDFfromMPinput(allMicrobes)
nodes=DFs$nodes
edges=DFs$edges
#get the visNetwork plot object:
vv=getVNPlotObject(nodes,edges,
addLegend=FALSE,
mainTitle='10 groups',
figWidth=800,
figHeight=800)
visOptions(vv)
## ---- results='hide'----------------------------------------------------------
microbes=c('Acetogens','Bacteroides','ButyrateProducers1')
out=microPopModel(microbeNames=microbes,
times=seq(0,2,0.01),
resourceSysInfo=resourceSysInfoHuman,
microbeSysInfo=microbeSysInfoHuman,
plotOptions = list(plotFig=FALSE),
networkAnalysis=TRUE)
## -----------------------------------------------------------------------------
DFs=networkDFfromMPoutput(chosen.time=1,MPoutput=out)
## -----------------------------------------------------------------------------
vv=getVNPlotObject(DFs$nodes,DFs$edges,scaleNodes=TRUE,scaleEdges = TRUE,
mainTitle='Network after 1 d',
figWidth = 500,figHeight = 500)
visOptions(vv)
## ---- results='hide'----------------------------------------------------------
microbes=c('Acetogens','Bacteroides','ButyrateProducers1')
out=microPopModel(microbeNames=microbes,
times=seq(0,2,0.01),
numStrains=c(Acetogens=1,Bacteroides=2,ButyrateProducers1=3),
strainOptions=list(randomParams=c('maxGrowthRate','halfSat'),percentTraitRange=20),
resourceSysInfo=resourceSysInfoHuman,
microbeSysInfo=microbeSysInfoHuman,
plotOptions = list(plotFig=FALSE),
networkAnalysis=TRUE)
## -----------------------------------------------------------------------------
DFs=networkDFfromMPoutput(chosen.time=1,MPoutput=out,sumOverStrains = FALSE)
vv=getVNPlotObject(DFs$nodes,DFs$edges,scaleNodes=TRUE,scaleEdges = TRUE,
figWidth = 700,figHeight = 700)
visOptions(vv)
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