aldex.plotFeature: Show dispersion of the expected values returned by...

In ggloor/ALDEx_bioc: Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

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,
  reset.par = 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
reset.par	reset the plotting parameter to par(c(1,1)), default FALSE

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")

ggloor/ALDEx_bioc documentation built on Oct. 31, 2023, 1:13 a.m.