Category: News

12-14 Sept 2016, Toulouse, FR (COST)

Our workshop in Toulouse (3-day) was sponsored by EU COST Action “The quest for tolerant varieties: phenotyping at plant and cellular level (FA1306). and organised by GenoToul Biostat platform, Laboratory of Plant-microbe Interactions (LIPM) and Plant Science Research Laboratory (LRSV). We trained and coached 26 participants and had a great time during the third day (‘byo’ data) and the ice breaking gala dinner!

 

mixomics-summer-school_09-2016-crop
Participants, organisers and tutors
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Looking very studious! We were hosted by the LIPM lab, INRA Auzeville Toulouse

Some feedback from our participants:

Overall I did enjoy the workshop, it was one of the most interesting and well put together that I have attended. Thank you very much.

The tutorials on the website are excellent for training.

It was a very good mixture of theory and practice to directly try out the methods. Also there were many experts who where available for questions. The presentations were quite clear to me as well as the course material and the provided scripts.

‘[Day 3] was useful, because it allows to check if we have well understood the use of each analysis, and bring our own data allows to make these analysis more concrete.’

[…] I could discuss with some other participants with similar experimental design and see how they think [they can] apply mixOmics

 

Data for Day 3 available:

Draught response in sunflower data with Get_started script (knitr format, open the .Rmd file with RStudio), with slides from David.

Some useful references discussed during the workshop:

Liu et al 2015: we used Principal Component Curves (a variant of PCA, but where you fit a curve, and where you need a ‘reference’ group) to quantify pathway regulation of Homologous Recombination in breast cancer.

Singh et al. 2016 (bioRxiv): the asthma study (#2) summarised some of the omics data sets into gene modules to quantify pathways before the integration step. This is the DIABLO paper.

Straube et al 2015: the linear mixed model framework to reduce the dimension of time course data from (n x p x T) to (T x p), lmms is available on CRAN.

Straube et al 2016: Dynomics to detect delay between time course data. Submitted.

Rengel et al. 2012 paper fr the drought response in sunflower.

Wickham 2014: tidy data

 

Version 6.1.0 and latest publications

We are proud to announce our new update 6.1.0 available on CRAN. It was supposed to be a small patch but we got slightly ahead of ourselves. Special thanks to the mixOmics French’Oz developers, Dr Florian Rohart (University of Queensland, Brisbane) and Mr François Bartolo (Université de Toulouse, France), as well as several users who have been using our latest methods and reported bugs or suggested improvements on our bitbucket issue website.

Manuscripts and publication update

  • Rohart F.,  Matigian N., Eslami A., Bougeard S and Lê Cao, K. A..MINT: A multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms. Now available on bioRxiv!

  • Singh A, Gautier B, Shannon C, Vacher M, Rohart F, Tebbutt S, K-A. Lê Cao. DIABLO – multi-omics data integration for biomarker discovery. Manuscript available in bioRxiv.

  • K-A. Lê Cao*, ME Costello*,  VA Lakis, F Bartolo, XY Chua, R Brazeilles, P Rondeau. (2016) MixMC: Multivariate insights into Microbial Communities.PLoS ONE 11(8): e0160169 [link]

List of changes in mixOmics 6.1.0 (in NEWS file)

In short,
– cimDIABLO argument ‘corThreshold’ replaced by ‘cutoff’
– new plots of tune and perf results now available
– tune function for block.splsda/DIABLO method
– auroc for supervised methods

New features:

1- auroc function applicable for (mint).(block).(s)plsda objects. AUc values also included in perf and tune functions (except mixDIABLO module)
2- tune.block.splsda function to chose the keepX parameters of block.splsda (a.k.a mixDIABLO)
3- plot for perf objects displays the classification error rate w.r.t components
4- plot for tune objects displays the classification error rate w.r.t keepX values (not implemented for tune.block.splsda)
5- multilevel function has been removed (as planned) as it is now included as an argument in other functions (see pca, pls, splsda, etc)

Enhancements:
1 – All tune functions (except for mixDIABLO/block.splsda module) include a ‘constraint’ argument to either build the model based on user input specific parameters (object$keepX.constraint) or based on the optimal parameter keepX determined by the tune function, see examples in help files.
2 – All perf functions (except for mixDIABLO/block.splsda module) have now a ‘constraint’ argument that allows the performances to be calculate either based on the number of parameters (object$keepX) defined in object or based on the variables selected on each component, see examples in help files.
3 – max.iter has been set to 100 to speed up computational time for all multivariate methods except pca/spca.
4 – cimDiablo: new arguments include transpose, row.names and col.names
5 – circosPlot: new arguments include var.names and comp. Argument ‘corThreshold’ has been replaced by ‘cutoff’.
6 – plotIndiv: new argument legend.title
7 – network function for block.spls(da) models and allows to plot for more than 2 blocks
8 – PCA: new argument ilr.offset to be used only for ILR log transform in PCA (mixMC module)
9 – Legend added in plotDiablo, new argument legend.ncol

Bug fixes:
1 – plotIndiv and ellipse: plot ellipse for all groups with more than 1 sample
2 – predict function: argument multilevel added, log transform included
3 – Call to plsda.vip() from the RVAideMemoire package
4 – other small bugs as listed in out bitbucket issues, matching rgl package changes.

Patch 6.0.1

We are preparing a patch to fix some small bugs we (and other users) noticed since we released version 6.0.0. The .zip (windows) and .tar.gz (linux / mac) can be downloaded from this page. We plan to push a completed patch on the CRAN end of august 2016.

Latest patch update: 18 August

Package to download: mixOmics_6.0.1.zip (windows) or mixOmics_6.0.1.tar.gz (linux, mac)

For the .tar.gz you can install it via RStudio (mac environment) alternatively, type in a terminal (linux environment):

R CMD INSTALL mixOmicsPatch_6.0.1.tar.gz

Then load the patch version in R:

#Load the patch 
library(mixOmics)

Bugs fixed:

Date: 18/08/2016

  • Offset value of 1 added for CLR log transform for mixMC
  • circosPlot variable name fixed for mixDIABLO, new argument size.variables
  • cimDiablo and circosPlot match name to legend color for mixDIABLO, new arguments transpose, row.names and col.names

Date: 03/08/2016

  • Call to plsda.vip() from the RVAideMemoire package
  • Speed up computations for PCA with logratio transformation
  • perf / tune for sPLS-DA with log ratio transformation (that will improve the performance of the model)
  • network function for block.spls models (still in development!)

Version 6.0.0

Dear mixOmics users,

It is with a huge relief and pride (and maybe some slight anticipatory anxiety of that very moment) that we announce the release of mixOmics_6_0_0 on CRAN. We are introducing three novel frameworks, mixMC, mixMINT and mixDIABLO, which are described (as best as we can, given the free remaining time we have on our hands not debugging) on the website. All manuscripts are in submission / revision so feel free to ask.

A special thanks to those who made that update possible, in particular Florian Rohart and Benoit Gautier, and the whole Lê Cao lab troop for the numerous layers of testing. We tested as much as we could but of course all data are different. Do no hesitate to report bugs or comments at mixomics[at]math.univ-toulouse.fr or on our bitbuket issue list.

Members of the mixOmics team will be present at the following summer conferences in the nothern hemisphere, feel free to say hello!
Rencontres R 2016: Toulouse, France, June 22-24, presentation on mixMINT
JOBIM 2016: Lyon, France, June 28-30, presentation on mixDIABLO
ISMB / ISCB 2016: Orlando, Florida, July 8 – July 12, attendance and presentation to the SBV crowd verification challenge, using our cousin package bootPLS
JSM 2016: Chicago, Illinois, July 30 – Aug 4, presentation on mixMC
INPPO 2016: Bratislava, Slovaquia, Sept 4-8, keynote

Below is the list of changes in the package. Please note the few argument names changes for some of the plots.

Changes in 6.0.0 (major, implementation improvements and new methods)

In short,

– argument names which changed in all plots for homogeneous call are: ‘main’ changed to ‘title’, ‘add.legend’ -> ‘legend’, ‘cex.xxx’ -> ‘size.xxx’, ‘plot.ellipse’ -> ‘ellipse’

– ncomp is now a single value in all wrapper. and block. functions (multiple integration)

Please refer to our help files for the functions listed below.

New features:

1- log.ratio transformation (log.ratio = c(‘CLR’, ‘ILR’)) in PCA and PLS-like methods to deal with compositional microbiome data (see website www.mixOmics.org/mixMC for details)

2 – plotLoadings is a novel graphical way of showing the regression coefficients of the selected variables (deprecated plotContrib)

3 – mixMINT module to analyse independent data sets on the same type of variable. See www.mixOmics.org/mixMINT for details.

      Added methods: mint.pls, mint.plsda, mint.spls, mint.splsda;

      S3 visualisations: plotIndiv, plotLoadings, plotVar;

      Performance evaluation: perf (new, uses leave one out group), tune (new, uses leave one out group)

4 – mixDIABLO module to integrate different omics data sets performed on the same samples. See www.mixOmics.org/mixDIABLO for details.

      Added methods: block.pls, block.plsda, block.spls, block.splsda;

      S3 visualisations: circosPlot (new), cimDiablo (new), plotDiablo (new), plotIndiv, plotLoadings, plotVar;   

      Performance evaluation: perf, tune, predict (new with majority vote for DIABLO, $vote)

5 – new data sets: stemcell (for MINT), TCGA.breast.cancer (for DIABLO)

Enhancements:

1 – plotIndiv: displays explained variance for sPLS objects

2 – multilevel option is now included in PLS and PCA objects (argument multilevel = design or sample information)

3 – WARNING: in all plots, homogeneous arguments call: ‘main’ changed to ‘title’, ‘add.legend’ -> ‘legend’, ‘cex.xxx’ -> ‘size.xxx’, ‘plot.ellipse’ -> ‘ellipse’

4 – print.method functions updated to show the range of graphics / other functions to use with the object

5 – predict function now outputs class names in $class

6 – data set vac18 reduced number of genes is now 100 genes

7 – plotContrib has been depraceted for plotLoadings

8 – ncomp input is now a single value in wrapper.rgcca, wrapper.sgcca, block.pls, block.spls, block.plsda, block.splsda

Bug fixes:

1 – explained variance for NIPALS/PCA fixed

2 – plot3d mistmatch legend color, double titles for plotIndiv ggplot2 and lattice, order of group for ggpot2 and lattice

3 – retired: data set prostate

Sept 12-14 Sept 2016, Toulouse, FR

Dear mixOmics users,

It is our pleasure to announce the following mixOmics 3-day workshop sponsored by EU COST Action “The quest for tolerant varieties: phenotyping at plant and cellular level (FA1306). More details in the pdf here. We do offer some travel grants for PhD students and early career researchers.

Organized by

 Dates:  Monday 12 September until Wednesday 14 September 2016 (3 full days)

Practical information: The course fee is 300 € for the academia and 600 € for the industry. It covers tuition, course material, coffee/tea, lunches and 1 diner downtown on Monday 12 September. Please note that no fee will be counted for 12 PhD students and/or early postdocs (up to 8 years after Ph.D) selected by COST Action FA1306, and their travel and living expenses will be take in charge up to 650 €.

Location: Toulouse, France

Maximum number of participants: 30

Deadline for application: 15 June 2016

Decision for attendee selection and grant allowance: 30 June 2016

Registration: 4 to 15 July 2016

Apply for this Summer School at: https://www.surveymonkey.com/r/FLSYJZP

In addition, send a CV to E Jamet (jamet [at] lrsv.ups-tlse.fr) and do not forget to mention if you want to apply for a grant.

Contact in Toulouse:  E Jamet, LRSV, jamet [at] lrsv.ups-tlse.fr

Good luck!

March 24-25 2016, Nantes, FR

This was our first workshop of the year!

‘many thanks for that great tutorial’, ‘excellent training, excellent teachers, excellent visual aids’

When : 24-25 March 2015

Where : Nantes

Institution : L’Ecole Nationale Vétérinaire, Agroalimentaire et de l’Alimentation Nantes-Atlantique (http://www.oniris-nantes.fr/)

Lab : Laboratoire d’Etude des Résidus et des Contaminants dans les aliments (http://www.oniris-nantes.fr/services/laberca/)

Teachers : Sébastien Déjean, François Bartolo (Toulouse-based team)

mixOmics for 2016

Well well, 2016 is well under way and we thought we could give you some heads up as of what is happening next for mixOmics.

2015 has been great for us:

  • We ran a total of 5 x 12-day mixOmics workshops (see list below, in Auckland NZ, Birsbane AUS, Paris, Montpellier and Toulouse, FR),
  • We launched our first shiny web-interface for sPLS-DA, which has been developed for our published paper (PCT patent ‘Blood Test for Throat Cancer’ PCT/AU2015/050723 on the biological findings of those interesting biomarkers). The shiny web-interface is still at its infancy, as we can only have one user at a time (shiny requirements!), and so if the interface goes grey, it means that someone else is using it!
  • Francois Bartolo, one mixOmics key developer from Toulouse, came to Brisbane for a 3-month visit and gave a good stab to most of the graphical functions (plotIndiv, network, CIM…)
  • Benoit Gautier, our key mixOmics developer based in Brisbane developed the shiny web-interface and set up the new sGCCA functions (integration of multiple data sets)
  • Benoit and Florian Rohart (also key mixOmics developer based in Brisbane) also worked together to push mixOmics V6.
  • We also made a good stab at our multivariate analysis pipeline for 16S microbial data, with a first unpublished workflow available here and a preprint available soon.

What’s planned for 2016?

  • More workshops! So far 3 are planned (those will be announced on our website)
  • We will clone few shiny web-interfaces on our virtual machine to enhance this tool.
  • mixOmics V6 is in the backlogs, with a planned update for end of April 2016 (stay tuned!) and we will (finally) push a proper mixOmics software manuscript.
  • We are in the process of reorganising a few workflows in mixOmics with:
    • mixMC: mixOmics for Microbial Communities (16S data)
    • mixDIABLO: a framework for Data Integration Analysis for Biomarker discovery using Latent variable approaches for multi-Omics studies (check out that acronym!)
    • mixMINT: mixOmics for Multi-group INTegrative studies to combine independent single ‘omics studies.

In short, there will be more functionalities for mixOmics users but it should not change the calls of the main functions and we are wrapping up the statistical developments that kept us busy in the last couple of years.

To be aware of our latest developments, please sign to our mailing list.

 

List of 2015 workshops:

  • Oct 24-25 2015 (2 days) AgroParisTech, Paris, France. #attendees: 22
  • Sept 15-16 2015 (2 days) National Institute for Agricultural Research, Toulouse, France. #attendees: 16
  • Sept 10-11 2015 (2 days) CIRAD, Agriculture research for development, Montpellier, France. #attendees: 25 (full)
  • 13-14 August 2015 (2 days) Translational Research Institute, Brisbane Australia. #attendees: 32 (full)
  • April 9-10 2015 (2 days) University of Auckland, New Zealand. #attendees: 40 (full)

mixOmics 5.2.0 (graphical improvements)

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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

Enhancements:
————-
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