proportionality {timeOmics} | R Documentation

## Proportionality Distance

### Description

`proportionality` is a wrapper that compute proportionality distance for a clustering result (`pca`, `spca`, `pls`, `spls`, `block.pls`, `block.spls`). and it performs a u-test to compare the median within a cluster to the median of the entire background set.

### Usage

    proportionality(X)

### Arguments

`X` | an object of the class: `pca`, `spca`, `pls`, `spls`, `block.pls` or `block.spls`

### Value

Return a list containing the following components:

`propr.distance` | Square matrix with proportionality distance between pairs of features
`propr.distance.w.cluster` | distance between pairs with cluster label
`pvalue` | Wilcoxon U-test p-value comparing the medians within clusters and with the entire background set

### 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

### See Also

`propr`

### 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)

[Package timeOmics version 1.0.1 Index]