vis.res {minet}R Documentation

Visualize Results

Description

A group of functions to plot precision-recall and ROC curves and to compute f-scores from the data frame returned by the validate function.

Usage

  pr(table)
  rates(table)
  fscores(table, beta=1)
  show.pr(table,device=-1,...)
  show.roc(table,device=-1,...)

Arguments

table This is a (steps x 5) matrix where steps is the number of thresholds used in the validation process and where columns contain TP,FP,TN,FN values (confusion matrix) as well as the threshold value used - see validate.
beta This is the weight of the recall in the f-score formula. Default: 1 (meaning precision as important as recall).
device The device to be used. This parameter allows the user to plot the results of various inferences on the same plotting window - see examples.
... arguments passed to plot

Value

The functions show.roc (show.pr) plots the ROC-curve (PR-curve) and returns the device used for the plot.
The function pr returns a (steps x 2) matrix where steps is the number of thresholds used in the validation process. The first column contains precisions and the second recalls.
The function rates also returns a (steps x 2) matrix where the first column contains true positive rates and the second column false positive rates.
The function fscores returns steps fscores according to the steps confusion matrices contained in the 'table' argument.

References

Patrick E. Meyer, Kevin Kontos, Frederic Lafitte, and Gianluca Bontempi. Information-theoretic inference of large transcriptional regulatory networks. EURASIP Journal on Bioinformatics and Systems Biology, 2007.

See Also

validate, plot

Examples

data(syn.data)
data(syn.net)
# Inference
mr <- minet( syn.data, method="mrnet", estimator="empirical" )
ar <- minet( syn.data, method="aracne", estimator="empirical" )
clr<- minet( syn.data, method="clr", estimator="empirical" )
# Validation
mr.tbl <- validate(mr,syn.net)
ar.tbl <- validate(ar,syn.net)
clr.tbl<- validate(clr,syn.net)
# Plot PR-Curves
max(fscores(mr.tbl))
dev <- show.pr(mr.tbl, col="green", type="b")
dev <- show.pr(ar.tbl, device=dev, col="blue", type="b")
show.pr(clr.tbl, device=dev, col="red",type="b")

[Package minet version 1.1.3 Index]