Multidimensional scaling informed by F-statistic: Visualizing microbiome for inference

Multidimensional scaling (MDS) is a dimensionality reduction technique for microbial ecology data analysis that represents the multivariate structure while preserving pairwise distances between samples. While its improvements have enhanced the ability to reveal data patterns by sample groups, these MDS-based methods require prior assumptions for inference, limiting their application in general microbiome analysis. In this study, we introduce a new MDS-based ordination, “F-informed MDS,” which configures the data distribution based on the F-statistic, the ratio of dispersion between groups sharing common and different characteristics. Using simulated compositional datasets, we demonstrate that the proposed method is robust to hyperparameter selection while maintaining statistical significance throughout the ordination process. Various quality metrics for evaluating dimensionality reduction confirm that F-informed MDS is comparable to state-of-the-art methods in preserving both local and ..., , # Multidimensional scaling informed by *F*-statistic: Visualizing grouped microbiome data with inference

* **Dataset DOI**: [10.5061/dryad.vmcvdnd3x](10.5061/dryad.vmcvdnd3x)
* **Software**: [https://github.com/soob-kim/FinfoMDS](https://github.com/soob-kim/FinfoMDS) \
(also *in prep* for Bioconductor submission)
* File or folder names are *italicized*. Package or variable names are `monospaced`. 

## File: Data.zip

##### **Description:** Raw data used in this study. Includes 3 folders and 1 file (see below).

1. Folder *Simulated* contains pairwise distances and ordination results from three simulated datasets. Includes 7 subfolders and 6 files.
* Six files are the original dataset and its associated labels set. The names are formatted as \"*sim*_<*x*>-<*type*>.*csv*\" where <*x*> is the replicate number and <*type*> indicates whether the file is the design matrix (\"*data*\") or response vector (\"*Y*\").
* Seven subfolders are grouped by the ordination method. Likewise, the file ...,