Graphical representation of SIMoNe outputs
Description
Plots various outputs associated to a SIMoNe run.
Usage
1 2 3 4 5 6 
Arguments
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 
Details
Here are some details about the plots possibly produced:

If
"BIC"
belongs to theoutput
argument, a plot representing the Bayesian Information Criterion as a function of each network inferred bysimone
is displayed. 
If
"AIC"
belongs to theoutput
argument, a ploy representing the Akaike Information Criterion as a function of each network inferred bysimone
is displayed. 
If
"ROC"
belongs to theoutput
argument andref.graph
is specified, the ROC curve (Receiver Operating Characteristic) is plotted by representing true positive rate vs. false positive rate. 
If
"PR"
belongs to theoutput
argument andref.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 theoutput
argument, a regularization path is plotted by representing the value of each entry of theTheta
matrix (that is, of each edge) vs. the penalty level lambda: there are as many values for the penalty as networks stocked in thesimone
objectx
. 
If
"path.edges"
belongs to theoutput
argument, a regularization path is plotted by representing the value of each entry of theTheta
matrix (that is, of each edge) vs. the degree of freedom inTheta
(that is, the number of edges in the current network). This is done for all the network stocked in thesimone
objectx
. 
If
"sequence"
belongs to theoutput
argument, an interactive plot is provided by starting from the empty network and adding the edges by successively covering the networks stocked in thesimone
objectx
.
Note
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).
Author(s)
J. Chiquet
See Also
simone
.
Examples
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)
