plot.eNetXplorer: generates plots from eNetXplorer object

Description Usage Arguments Author(s) See Also Examples

View source: R/plot.eNetXplorer.R

Description

This function is a wrapper for a variety of plots, namely:

summary: model performance across alpha (to assess the relative performance among different member models in the elastic net family, as well as in relation to permutation null models);

lambdaVsQF: given alpha, quality function across lambda (to examine the selection of the optimal penalty parameter);

measuredVsOOB: given alpha, response vs out-of-bag predictions across instances (to assess individual instances, examine outliers, etc);

contingency: (for categorical models) given alpha, response vs out-of-bag predictions across classes;

featureCaterpillar: given alpha, caterpillar plot of feature statistics compared to permutation null models (with statistical significance annotations for individual features); and

featureHeatmap: heatmap of feature statistics across alpha (including statistical significance annotations for individual features).

Usage

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## S3 method for class 'eNetXplorer'
plot(x, plot.type=c("summary","lambdaVsQF","measuredVsOOB","contingency",
"featureCaterpillar","featureHeatmap"), alpha.index, stat=c("freq","coef"), ...)

Arguments

x

eNetXplorer object.

plot.type

Type of plot to be produced. Available plots are "summary", "lambdaVsQF", "measuredVsOOB", "contingency" (categorical models only), "featureCaterpillar" and "featureHeatmap".

alpha.index

Integer indices to select alpha values. Default is 1:length(alpha)

stat

Feature statistic: "freq" for nonzero frequency, "coef" for mean nonzero coefficient. Used for plot types "featureHeatmap" and "featureCaterpillar", ignored otherwise.

...

Additional plotting parameters.

Author(s)

Julian Candia and John S. Tsang
Maintainer: Julian Candia [email protected]

See Also

eNetXplorer, plotSummary, plotLambdaVsQF, plotMeasuredVsOOB, plotContingency, plotFeatureCaterpillar, plotFeatureHeatmap

Examples

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## Not run: 
data(QuickStartEx)
fit = eNetXplorer(x=QuickStartEx$predictor, y=QuickStartEx$response,
family="gaussian", n_run=20, n_perm_null=10, seed=111)

plot(x=fit,plot.type="summary")
plot(x=fit,plot.type="lambdaVsQF",alpha.index=2)
plot(x=fit,plot.type="measuredVsOOB",alpha.index=c(1,3,5))
plot(x=fit,plot.type="featureCaterpillar",stat="coef")
plot(x=fit,plot.type="featureHeatmap",stat="freq")

## End(Not run)

juliancandia/eNetXplorer documentation built on April 22, 2018, 9:20 p.m.