aldex.plotFeature {ALDEx2}R Documentation

Generate dispersion, difference, and effect density plots for a feature, given an aldex Object

Description

Calculates dispersion, difference, and effect vectors from the given aldex object for the selected feature. Generates plots for each group's pooled dispersion vector, the element-wise absolute difference between groups, and the effect size of the difference between groups.

Usage

    ## S3 method for class 'plotFeature'
aldex(clrData, featureName, pooledOnly=FALSE,
                                  densityOnly=FALSE)

Arguments

clrData

an object of class aldex produced by the aldex function

featureName

the name of the feature to generate plots for, provided as a string

pooledOnly

a logical value to generate only the pooled dispersion vector plot

densityOnly

a logical value to toggle the boxplots overlaid on each plot

Details

The dispersion, difference, and effect size vectors are defined in (Fernandes et al. (2018). A reproducible effect size is more useful than an irreproducible hypothesis test to analyze high-throughput sequencing datasets. Preprint at https://arxiv.org/abs/1809.02623).

Value

None.

References

Please use the citation given by citation(package="ALDEx").

See Also

aldex, aldex.clr

Examples

    data(selex)
        #subset for efficiency
        selex <- selex[1201:1600,]
    conds <- c(rep("NS", 7), rep("S", 7))
    x <- aldex.clr(selex, conds, mc.samples = 128, denom = "all", verbose = FALSE)
    aldex.plotFeature(x,"T:E:K:D")
[Package ALDEx2 version 1.18.0 Index]