Plots various outputs associated to a SIMoNe run.
1 2 3 4 5 6 
x 
output of a 
output 
a vector of character string indicating which outputs must be plotted
(picken from 
ref.graph 
a network of reference provided through an adjacency matrix that is
used to compute the ROC and PR curves. Only required if 
ask 
a logical indicating if the graphics device should be
interactive. Default is 
... 
Additonal arguments for generic 
Here are some details about the plots possibly produced:
If "BIC"
belongs to the output
argument, a plot
representing the Bayesian Information Criterion as a function of
each network inferred by simone
is displayed.
If "AIC"
belongs to the output
argument, a ploy
representing the Akaike Information Criterion as a function of
each network inferred by simone
is displayed.
If "ROC"
belongs to the output
argument and
ref.graph
is specified, the ROC curve (Receiver
Operating Characteristic) is plotted by representing true positive
rate vs. false positive rate.
If "PR"
belongs to the output
argument and
ref.graph
is provided by the user, the PR curve
(Precision/Recall) is plotted by representing positive predicted
values vs. true positive rate.
If "path.penalty"
belongs to the output
argument, a
regularization path is plotted by representing the value of each
entry of the Theta
matrix (that is, of each edge) vs. the
penalty level lambda: there are as many values for
the penalty as networks stocked in the simone
object x
.
If "path.edges"
belongs to the output
argument, a
regularization path is plotted by representing the value of each
entry of the Theta
matrix (that is, of each edge) vs. the
degree of freedom in Theta
(that is, the number of edges in the
current network). This is done for all the network stocked in the
simone
object x
.
If "sequence"
belongs to the output
argument, an
interactive plot is provided by starting from the empty network and
adding the edges by successively covering the networks stocked in
the simone
object x
.
If the user asked for "PR"
and "ROC"
curves yet did not specify a
network of reference, these curves will not be plotted (no warning or
error will be specified).
J. Chiquet
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18  ## data set and network generation
g < rNetwork(p=50, pi=50)
data < rTranscriptData(300,g)
attach(data)
## running simone
res < simone(X, type="steadystate")
## plotting the results: just the ROC curve
plot(res, output=c("ROC"), ref.graph=g$A)
## plotting the results: just the path as a function of the penalty
plot(res, output=c("path.penalty"), main="I want to put my own title")
## plotting the results: everything possible (the default)
plot(res)
detach(data)

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