mixOmics

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plotLoadings issue

2

Dear MixOmics team, I have completed an analysis by using DIABLO. Two blocks, mRNA and protein. When I tried to plot the loadings and their contributions, only one block information...

aldosc

**Is your feature request related to a problem? Please describe.** A `block.spls` object cannot be passed into `cim()`, despite the fact that the functionality already exists to produce a CIM...

Max-Bladen

mixOmics 6.17.26 build failing on Bioconductor

2

* see http://bioconductor.org/checkResults/devel/bioc-LATEST/mixOmics/ * see https://github.com/mixOmicsTeam/mixOmics/runs/3753496049?check_suite_focus=true

aljabadi

OPLS-DA

2

Is it possible to implement OPLS-DA (orthogonal Partial least squares-discriminant analysis) in mixOmics? I like the nice output of mixOmics, but it doesn't have OPLS-DA compared to ropls.

rhhu

t.test.process choice ignores bounded nature of performance criteria

1

many times users have complained that the chosen keepX is too strict. Here's an example for `tune.spca` for component 2: ``` r suppressMessages(library(mixOmics)) data(multidrug) set.seed(2341) tune.spca_res1 KeepX = 5 #>...

aljabadi

Out of date information and source code in online vignette

1

Please follow **all the steps** described at https://mixomics-users.discourse.group/t/reproducible-example-to-clarify-issues/470 and next fill in the items below: ------------ 🐞 **Describe the bug:** I tried to tune the parameter for my SPLS models,...

jamesjiadazhan

This PR contains numerous changes to the `network()` function. Users noted that a lack of control over vertex size and distances made for difficulty in plotting. Vertices frequently overlapped, covering...

Max-Bladen

**Is your feature request related to a problem? Please describe.** Users have had trouble with using the `network()` function as the vertices begin to overlap ([see here](https://mixomics-users.discourse.group/t/change-network-layout/1007)). The vertices completely...

Max-Bladen

No parallelization in tune.spls

2

------------ 🐞 **Describe the bug:** tune.spls is not using multicore processing even with BPPARAM set correctly. ------------ 🔍 **reprex results from [reproducible example](https://mixomics-users.discourse.group/t/reproducible-example-to-clarify-issues/470) including sessioninfo():** Monitoring of this code from...

EmileFaure

feature request: use renv for dependency management

1

Using [renv](https://rstudio.github.io/renv/articles/renv.html) will ensure a better and more consistent development experience.

aljabadi