Create an importance graph from a bootstrapping result of a single classification method.

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Description

After running bsSCAD, bsPAMR or bsRFBORUTA, the final feature ranking is shown as egg-shaped graph using this function.

Usage

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makeIG(res_bstr, SUBDIR=NULL, prob=.975)

Arguments

res_bstr

Result list from PAMR, SCAD or RF_Boruta bootstrapping.

SUBDIR

Where to store the output. If NULL, the importance graph is plotted to the standard plotting device.

prob

Quantile in [0,1], defines the cutoff, at which frequency of cooccuring features an edge will be drawn between the two features in the importance graph.

Details

For any bootstrapping feature selection a result list is generated. The observed feature sets during all of the bootstrapping runs are combined into a graph representing the number of occurrences of a feature as nodes, as well as the cooccurrences of pairs of features as edges. The width of the nodes is proportional to their frequency of occurrence, the width of the edges proportional to the number of cooccurrences of two features in all boostrapping feature sets. Edges are drawn for the top 10

Value

A list with three elements:

allsignatures

All bootstrapping feature sets.

allprots

Union of all features that occur in any feature set.

adj

An adjacency matrix with the counts of (co)occurrences.

Author(s)

Christian Bender (christian.bender@tron-mainz.de)

See Also

doBS bsSCAD bsPAMR bsRFBORUTA

Examples

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## Not run: 
# library(bootfs)
set.seed(1234)
data <- simDataSet(nsam=30, ngen=100, sigma=2, plot=TRUE)
logX <- data$logX
groupings <- data$groupings

## run the bootstrapping
retBS <- doBS(logX, groupings, 
	fs.methods=c("pamr","scad","rf_boruta"),
	DIR="bs", 
	seed=123, bstr=5, saveres=FALSE, jitter=FALSE,
	maxiter=100, maxevals=50, bounds=NULL,
	max_allowed_feat=NULL, n.threshold=50,
	maxRuns=30)

## summarize a single bootstrapping run into an importance graph
bsres <- makeIG(retBS[[1]], SUBDIR=NULL, prob=.975)

## remove the created directory
system("rm -rf bs")


## End(Not run)

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