Description Usage Arguments Details Value See Also Examples
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | 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
1 2 3 4 5 6 7 8 | 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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