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]