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

Multidimensional scaling (MDS) is a widely used dimensionality reduction technique in microbial ecology data analysis that captures the multivariate structure of the data while preserving pairwise distances between samples. While improvements in MDS have enhanced the ability to reveal group-specific data patterns, 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 method, \"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 semisynthetic 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 preserv..., , # Multidimensional scaling informed by *F*-statistic: Visualizing grouped microbiome data with inference

* **Software**: [https://bioconductor.org/packages/FinfoMDS](https://bioconductor.org/packages/FinfoMDS)
* File or folder names are *italicized*. Package or variable names are `monospaced`. 

## File: Data.zip

##### **Description:** Raw data used in this study. Includes 4 folders and 4 files (see below).

1. Folder *Simulated*
* Contains pairwise distances and ordination results. Includes 6 subfolders and 20 files. See below.
* Folder *F-MDS* contains traning log by epoch (folder *TrainingLog*) and resulting representations `Z` (folder *Results*).
* File names inside the folder are formatted as \"*sim_rev_{x}-N{n}-{method}-{param}-{type}.csv*\". Formatting rule is described in table below.
* \"*-Z.csv*\" file is tabulated by each sample and its location in 2D coordinate in each row and column, respectively.
* \"*-log.csv*\" file is tabulated at each row by training e..., , **Changes after May 7, 2025:** 

## File: Data.zip

#### Folder `Alga` and files `alga.R`, `simulated.R`, `ternary.R` have newly been added. Folders `Simulated` and `Ternary` have been revised.

#### Newly added files/folders

1. Folder *Alga*
* Ordination results from algal microbiome dataset (Kim et al., 2022).
* Microbiome dataset can be obtained elsewhere, e.g., [https://github.com/soob-kim/FinfoMDS](https://github.com/soob-kim/FinfoMDS)
2. File *alga.R*
3. File *simulated.R*
4. File *ternary.R*

#### Revised folders

1. Folder *Simulated*
* Previous 6 files have been replaced with new 20 files.
* The replacement represents new simulation datasets with revised conditions, i.e., data size, dimension.
* Previous folder `MDS` has been removed as it is not used in revised manuscript version.
* All other folders (`F-MDS`, `Isomap`, `superMDS`, `t-SNE`, `UMAP-S`, `UMAP-U`) contains newly replaced files after performing the ordinations with the new simulation da...