README.md

In JeffreyMolendijk/ml-viewR: Machine learning viewer

mlview

mlview is a visualization package for machine learning analyses. The functions in mlview are named according to the package which they are to be used with, whereas generic functions start with "mlview".

ropls

This package contains functions used for visualization of ropls objects. mlview currently supports all models created by ropls, including PCA, PLS, OPLS, PLS-DA and OPLS-DA models.

The ropls.plot function can be used to create score (default) and loading plots. This function allows colour by group and the addition of group ellipses. Hotelling's T2 ellipse can be toggled on or off. The ggplot output from ropls.plot can be further modified if required.

The ropls.enrich function performs fgsea enrichment on a matrix of variables, variable information and a single numeric column. Furthermore, the column(s) used in the enrichment analysis can be specified. This function returns the fgsea output, including enriched groups, enrichment scores and p-values.

Citation for ropls: Thevenot, E.A., Roux, A., Xu, Y., Ezan, E., Junot, C. 2015. Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. Journal of Proteome Research. 14: 3322-3335.

JeffreyMolendijk/ml-viewR documentation built on Oct. 30, 2019, 7:37 p.m.