View source: R/proprotionality.R
proportionality | R Documentation |
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.
proportionality(X)
X |
an object of the class: |
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 |
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
propr
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)
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