% 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

}