plotFeatureCaterpillar: generates caterpillar plot of feature statistics

In juliancandia/eNetXplorer: Quantitative Exploration of Elastic Net Families for Generalized Linear Models

generates caterpillar plot of feature statistics

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

plotFeatureCaterpillar(x, alpha.index=NULL, stat=c("freq","coef"), 
feature.all=FALSE, feature.pval.thres=NULL, feature.set=NULL, feature.top.n=25, 
signif.code=TRUE, 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=TRUE, ...)

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 [e-mail]

See Also

eNetXplorer, plot

Examples

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")

juliancandia/eNetXplorer documentation built on May 11, 2023, 1:59 a.m.