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.
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.
- 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: Six different analyses were provided using the Wilcoxon Rank Sum test, t-test, metagenomeSeq, DESeq2, Limma-Voom, edgeR, LEfSe, MaAsLin3. These will perform statistical analysis and generate plots and summary tables based on the significant taxa.
- 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.
*It provides publication quality plots in seven formats: JPG, TIFF, PDF, SVG, BMP, EPS, and PS and summary tables (.csv format) to visualize and 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.