--- a
+++ b/man/proportionality.Rd
@@ -0,0 +1,46 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/proprotionality.R
+\name{proportionality}
+\alias{proportionality}
+\title{Proportionality Distance}
+\usage{
+proportionality(X)
+}
+\arguments{
+\item{X}{an object of the class: \code{pca}, \code{spca}, \code{pls}, \code{spls}, \code{block.pls} or \code{block.spls}}
+}
+\value{
+Return a list containing the following components:
+  \item{propr.distance}{Square matrix with proportionality distance between pairs of features}
+  \item{propr.distance.w.cluster}{distance between pairs with cluster label}
+  \item{pvalue}{Wilcoxon U-test p-value comparing the medians within clusters and with the entire background set}
+}
+\description{
+\code{proportionality} is a wrapper that compute proportionality distance for 
+a clustering result (\code{pca}, \code{spca}, \code{pls}, \code{spls}, \code{block.pls}, \code{block.spls}).
+and it performs a u-test to compare the median within a cluster to the median of the entire background set.
+}
+\examples{
+demo <- suppressWarnings(get_demo_cluster())
+
+# pca
+X <- demo$pca
+propr.res <- proportionality(X)
+plot(propr.res)
+
+# pls
+X <- demo$spls
+propr.res <- proportionality(X)
+plot(propr.res)
+
+# block.pls
+X <- demo$block.spls
+propr.res <- proportionality(X)
+plot(propr.res)
+
+}
+\references{
+Lovell, D., Pawlowsky-Glahn, V., Egozcue, J. J., Marguerat, S., Bähler, J. (2015). Proportionality: a valid alternative to correlation for relative data. PLoS Comput. Biol. 11, e1004075. doi: 10.1371/journal.pcbi.1004075
+
+Quinn, T. P., Richardson, M. F., Lovell, D., Crowley, T. M. (2017). propr: an r-package for identifying proportionally abundant features using compositional data analysis. Sci. Rep. 7, 16252. doi: 10.1038/s41598-017-16520-0
+}