aldex.plotFeature {ALDEx2} | R Documentation |
aldex
Object
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.
## S3 method for class 'plotFeature' aldex(clrData, featureName, pooledOnly=FALSE, densityOnly=FALSE)
clrData |
an object of class |
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 |
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).
None.
Please use the citation given by citation(package="ALDEx")
.
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")