Al J Abadi

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

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 #>...

feature request: use renv for dependency management

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

feature request: Repel labels in plotIndiv and plotVar

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Would be good if the plots could take a `repel=` arg with `style='ggplot2'`. Use code below as guide to what should work. See https://mixomics-users.discourse.group/t/repel-labels-in-plotindiv-and-plotvar/621 ```r data(nutrimouse) X

We should either prohibit the condition or handle it more efficiently. `stratified.subsampling` is also unnecessarily lengthy. ``` r data(liver.toxicity) X UseMethod("perf") #> ``` Created on 2021-02-16 by the [reprex package](https://reprex.tidyverse.org)...

Add background.predict support for mint.splsda

1

Hi, trying to perform this: ``` data(stemcells) res = mint.splsda(X = stemcells$gene, Y = stemcells$celltype, ncomp = 3, study = stemcells$study) background = background.predict(res, comp.predicted = 2, dist = "max.dist")...

See https://github.com/mixOmicsTeam/mixOmics/issues/109

To address #30. It is better to default on `return.call=FALSE` to avoid unnecessary excessive memory usage.

The performance of the `tune.mint.splsda` model at optimum hyperparameters: ```r data(stemcells) X = stemcells$gene Y = stemcells$celltype study

plotArrow Error: Aesthetics must be either length 1 or the same as the data

2

See https://mixomics-users.discourse.group/t/error-in-plotarrow-of-splsda/689