aldex.plotFeature {ALDEx2}R Documentation

Show dispersion of the expected values returned by aldex.effect

Description

aldex.plotFeature generates density plots showing the dispersion of the expected values given in the output from aldex.effect. The expected values are shown in the plots. This is a diagnostic visualization to help determine if the expected values are trustworthy

Usage

aldex.plotFeature(
  clrData,
  featureName,
  pooledOnly = FALSE,
  densityOnly = FALSE
)

Arguments

clrData

the output object from aldex.clr

featureName

the name of the feature from the input data

pooledOnly

show only the pooled plots, default FALSE, shows all plots

densityOnly

show only the density plots, default FALSE includes expected values

Author(s)

Brandon Lieng, Greg Gloor

References

Please use the citation given by citation(package="ALDEx2").

See Also

aldex.clr, aldex.effect, selex

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=4, denom="all")
aldex.plotFeature(x, "S:D:A:D")
[Package ALDEx2 version 1.20.0 Index]