MetaDAVis
Introduction
MetaDAVis (interactive Metagenome Data Analysis and Visualization) is a browser-based and user-friendly R Shiny application for researchers without programming proficiency to analyze and visualize metagenomics results from kingdom to species level. It comprises six functional analyses and one bulk download utility.
The package includes the following:- Data summary and abundance distribution The data can be visualized in the stacked bar plot for abundance percentage, value, and relative frequency from 2 to 100 Taxa.
- Group: Samples are grouped by given conditions based on the metadata.
- Individual: Sample-based plots.
- Diversity analysis
- Alpha: Seven different methods was used from the phyloseq package. The results were displayed in a box and violin plot with a summary table.
- Beta: A total of 42 different diversity metrics were integrated from the phyloseq (unlist(distanceMethodList)) package with six selection methods. Results are visualized by bar and ordination with a summary table. Boxplot Wilcoxon p-values and the PERMANOVA p-value can be shown on the plot.
- Dimension reduction
- PCA: The ggfortify and plotly package was used to display plots in 2D(with and without labels and frame) and 3D with their summary table.
- t-SNE: Six different methods was used from the scater package. The samples were displayed in a t-SNE plot (2 and 3 dimensions) with a summary table.
- UMAP: Six different methods was used from the scater package. Displays the UMAP plot in sample and cluster-based with a summary table.
- Correlation analysis
- Taxa-based: The ggfortify package was used to display plot (with and without labels and frame) and their summary table.
- Sample-based: Six different methods was used from the scater package. The result was displayed in 2 and 3 dimensions t-SNE plots with a summary table.
- Heatmap: It was integrated with the ComplexHeatmap package. Display heatmap with and without row and column dendrograms and names.
- Differential abundance
- Two groups: Eight different analyses were provided using the Wilcoxon Rank Sum test, t-test, metagenomeSeq, DESeq2, Limma-Voom, edgeR, LEfSe, and MaAsLin3. Fold-change results are interpreted as condition2/condition1, and the condition selected in condition1 is removed from the condition2 choices.
- Individual box plots in differential analysis display up to 25 significant taxa per image using a 5 column by 5 row layout. When more than 25 significant taxa are available, each plot image can be selected and downloaded separately.
- Multiple groups comparison: Two different analyses, such as Kruskal-Wallis test and ANOVA was used for more than multiple group comparisons. These will perform statistical analysis and generate plots and summary tables based on the significant taxa.
- Bulk download
- The Bulk Download menu exports all completed analysis images and tables in one structured ZIP folder. The Completed Outputs panel lists the analyses that will be included, users can choose JPG, PNG, TIFF, PDF, SVG, BMP, EPS, or PS for plots, differential individual plot pages are exported as separate image files, tables are saved as CSV files, MaAsLin3 output ZIP is included when available, sessionInfo.txt is added for reproducibility, and bulkDownload_warnings.txt is added if any completed output cannot be exported.
*It provides publication quality plots in multiple formats and summary tables (.csv format) to visualize, download individually, or export together through Bulk Download.
use MetaDAVis online
MetaDAVis is deployed at: https://www.gudalab-rtools.net/MetaDAVis
Launch MetaDAVis using R and GitHub
MetaDAVis were deposited under the GitHub repository: https://github.com/GudaLab/MetaDAVis
Before running the app, the user must have R (>= 4.4.2), RStudio (>= 2024.12.0), Bioconductor (>= 3.20) and Shiny (>= 1.10.0) (Tested with this version).
If users use an older R version, they may encounter errors in installing packages, So the users are recommended to update their R version first.
Once the user opens the R in the command line or Rstudio, need to run the following command in R to install the shiny package.
install.packages('shiny')
library(shiny)
Start the app
Start the R session using RStudio and run these lines:shiny::runGitHub('MetaDAVis','GudaLab')
or
Alternatively, download the source code from GitHub and run the following command in the R session using RStudio:
library(shiny)
runApp('/path/to/the/MetaDAVis-master', launch.browser=TRUE)
Help manual for the usage of MetaDAVis [Download]
Cite:
Jagadesan S, Guda C (2025) MetaDAVis: An R shiny application for metagenomic data analysis and visualization. PLoS ONE 20(4): e0319949. https://doi.org/10.1371/journal.pone.0319949
Developed and maintained by
This application was created by Sankarasubramanian Jagdesan and Babu Guda. We share the passion about developing an user-friendly tool for all biologists, especially those who do not have access to bioinformaticians or programming efficency.
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