plotCurves2 | R Documentation |
The generic function plotCurves2
plots the growth curves and concentration changes of the most changing substances from simulation steps in an Eval
object using maximally distinct colors.
plotCurves2(
object,
legendpos = "topleft",
ignore = c("EX_h(e)", "EX_pi(e)", "EX_h2o(e)"),
num = 10,
phencol = FALSE,
biomcol = FALSE,
dict = NULL,
subs = list(),
growthCurve = TRUE,
subCurve = TRUE
)
## S4 method for signature 'Eval'
plotCurves2(
object,
legendpos = "topright",
ignore = c("EX_h(e)", "EX_pi(e)", "EX_h2o(e)"),
num = 10,
phencol = FALSE,
biomcol = FALSE,
dict = NULL,
subs = list(),
growthCurve = TRUE,
subCurve = TRUE
)
object |
An object of class Eval. |
legendpos |
A character variable declaring the position of the legend |
ignore |
A list of character variables with substance names that sould be omitted in the plot |
num |
An integer defining the number of substrates to be plot |
phencol |
Boolean variable indicating whether phenotypes should be higlighted |
biomcol |
A boolean indicating if biomass should be included in gowth curve |
dict |
List defining new substance names. List entries are intepreted as old names and the list names as the new ones. |
subs |
List of substance names. If empty, substances with highest variance will be used. |
growthCurve |
True if growth curve should be shown (default TRUE) |
subCurve |
True if substance curve should be shown (default TRUE) |
The parameter retdata
can be used to access the data used for the returned plots to create own custom plots.
Returns two graphs in one plot: the growth curves and the curves of concentration changes
Eval-class
and Arena-class
data(Ec_core, envir = environment()) #get Escherichia coli core metabolic model
bac <- Bac(Ec_core,deathrate=0.05,
minweight=0.05,growtype="exponential") #initialize a bacterium
arena <- Arena(n=20,m=20) #initialize the environment
arena <- addOrg(arena,bac,amount=10) #add 10 organisms
arena <- addSubs(arena,40) #add all possible substances
eval <- simEnv(arena,5)
plotCurves2(eval)
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