mixOmics 5.2.0 (graphical improvements)


The reality of R packages development. From http://www.r-bloggers.com/introducing-the-reproducible-r-toolkit-and-the-checkpoint-package/


We are proud to introduce a new mixOmics update dedicated mainly to improvements in graphical outputs. The changes are listed below, please note the change of arguments names (promise, we’ll try not do that again). More posts to come about the new functionalities.

We are particularly grateful to our key contributors Mr Francois Bartolo (Université de Toulouse, who is doing a short stay down here in Brisbane) and Dr Florian Rohart (University of Queensland) for doing such a great job with the development, debugging and testing. If we have missed something please let us know!

New features:
1 – plotArrow for PLS, sPLS, rCC, rGCCA, sGCCA, sGCCDA is an improved version from our old s.match function (which is still available but will be soon deprecated)
2 – network function has been enhanced with various options to represent the nodes (e.g. lty.edge=’dotted’,row.names = FALSE), see our website for more examples
2 – rcc has a new argument method = c(“ridge”, “shrinkage”) with shrinkage to estimate the shrinkage coefficients directly
3 – plotIndiv directly implements 3d plots (style=’3d’), including ellipses, % of variance explained output for PCA, centroids and star plots (see example(plotIndiv))
4 – plotVar directly implements 3d plots (style=’3d’), legend can also be added with add.legend = TRUE
5 – cim and network have new arguments: save = c(‘jpeg’,’tiff’,’png’,’pdf’) to save plots directly, and name.save. Argument threshold has been added/updated for both displays. Some arguments underwent name changes, see ?network

1 – network: a single function for all objects.
2 – pheatmap.multilevel has been deprecated with the new enhancements of CIM
3 – plot3dIndiv and plot3dVar have been deprecated (see new features in plotIndiv and plotVar)
4 – plotContrib also now available for sgccda plsda, splsda objects. Added arguments coplete.name.var and col.ties (see ?plotContrib), changed argument name ties to show.ties
5 – imageMap has been deprecated (now included in cim directly)
6 – pca also outputs ‘loadings’ and ‘variates’ to remain in the mixOmics spirit
7 – tau.estimate help file removed as now directly called as internal function from rcc and srgcca
8 – imgCor: added argument ‘main’ and changed argument names x.sideColors and y.sideColors to sideColors
9 – cim: changed argument names labRow and labCol to row.sideColors and col.sideColors

Bug fixes:
1 – plotContrib now fixed (showed wrong contribution colors)
2 – cim has been fixed to show the ordered variable names after users reports (thanks!)
3 – resolved blank page in network when saving image as a pdf

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