plotFeatureCaterpillar: generates caterpillar plot of feature statistics

Description Usage Arguments Details Author(s) See Also Examples

View source: R/plotFeatureCaterpillar.R

Description

Given alpha, this function generates a caterpillar plot of feature statistics compared to permutation null models, which includes statistical significance annotations for individual features. By default, features are selected (and ordered top-down) by statistical significance; options are provided to customize feature selection and display.

Usage

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plotFeatureCaterpillar(x, alpha.index=NULL, stat=c("freq","coef"), feature.all=F, 
feature.pval.thres=NULL, feature.set=NULL, feature.top.n=25, signif.code=T, 
xlab=NULL, ylab=NULL, main=NULL, col.main="black", cex.main=0.85, line=1.5, 
subtitle=NULL, col.subtitle="darkgray", line.subtitle=0.5, cex.subtitle=0.55, 
cexRow=NULL, cex.lab=0.95, legend=T, ...)

Arguments

x

eNetXplorer object.

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.

feature.all

(Feature selection argument 1) Logical to show all features. Default is FALSE.

feature.pval.thres

(Feature selection argument 2) P-value threshold to select features. Default is NULL.

feature.set

(Feature selection argument 3) Character vector of feature names to display. Default is NULL.

feature.top.n

(Feature selection argument 4) Number of top features (ordered by p-value) to display. Default is 25.

signif.code

Logical to display significance annotations. Default is TRUE.

xlab

Label for x axis.

ylab

Label for y axis.

main

Custom title.

col.main

Title color.

cex.main

Title size.

line

Title location.

subtitle

Custom subtitle.

col.subtitle

Subtitle color.

line.subtitle

Subtitle location.

cex.subtitle

Subtitle size.

cexRow

Size of row labels.

cex.lab

Axis label size.

legend

Logical to display legend. Default is TRUE.

...

Additional plotting parameters.

Details

Feature selection criteria are hierarchical based on arguments 1 through 4 (see argument description above), with argument 1 at the top of the hierarchy. E.g. if feature.all is explicitly set to TRUE, it will take precedence over any other feature selection argument. By default, the top 25 features are displayed, ordered top-down by significance based on the given value of alpha.

Author(s)

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

See Also

eNetXplorer, plot

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="featureCaterpillar",stat="coef")
plotFeatureCaterpillar(x=fit,alpha.index=3,stat="coef",main="custom title")

## End(Not run)

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