plot.simone: Graphical representation of SIMoNe outputs

Description

Plots various outputs associated to a SIMoNe run.

Usage

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## S3 method for class 'simone'
plot(x,
     output    = c("BIC", "AIC", "ROC", "PR", "path.edges",
                   "path.penalty", "sequence"),
     ref.graph = NULL,
     ask       = TRUE,  ...)

Arguments

x

output of a simone run (must be an object of class simone)

output

a vector of character string indicating which outputs must be plotted (picken from "BIC", "AIC", "ROC", "PR", "path.edges", "path.penalty" or "sequence"). Default is to plot everything possible.

ref.graph

a network of reference provided through an adjacency matrix that is used to compute the ROC and PR curves. Only required if "ROC" and "PR" belongs to the output argument.

ask

a logical indicating if the graphics device should be interactive. Default is TRUE.

...

Additonal arguments for generic plot (such as main = "my title").

Details

Here are some details about the plots possibly produced:

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

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## data set and network generation
g    <- rNetwork(p=50, pi=50)
data <- rTranscriptData(300,g)
attach(data)

## running simone
res <- simone(X, type="steady-state")

## 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)

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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