README.md

EasyPubPlot - Easy and Publishable Ploting

An interactive, customizable, and coding-free Shiny App to easily create publishable plots for scientific papers. EasyPubPlot is freely available at https://pharmaco-omicslab.shinyapps.io/EasyPubPlot.

App Interface

Example

Install and run locally

EasyPubPlot requires

Step 1: Check and install the necessary packages from CRAN to run EasyPubPlot.

for (pkg in c("remotes", "shiny", "shinyjs", "shinyWidgets", "colourpicker", "bslib", "shinytoastr", "dplyr", "magrittr", "ggplot2", "tibble", "tidyr", "ggthemes", "BiocManager", "circlize", "ggiraph")) {
  if (!require(pkg, character.only = TRUE)) {
    install.packages(pkg, dependencies = TRUE)
  }
}

Step 2: Check and install the necessary packages from BiocManager to run EasyPubPlot.

for (pkg in c("EnhancedVolcano", "ComplexHeatmap")) {
  if (!require(pkg, character.only = TRUE)) {
    BiocManager::install(pkg, dependencies = TRUE)
  }
}    

Step 3: Install EasyPubPlot.

remotes::install_github("Pharmaco-OmicsLab/EasyPubPlot")

Step 4: Run EasyPubPlot in your computer.

Run this code

library(EasyPubPlot)  
runEasyPubPlot()     

Or run this code to use interactive plot mode (support volcano and bubble plots)

library(EasyPubPlot)  
runInteractiveEasyPubPlot()     

Citation

Nguyen Tran Nam Tien, Nguyen Quang Thu, Dong Hyun Kim, Seongoh Park#, Nguyen Phuoc Long#. "EasyPubPlot: a shiny web application for rapid omics data exploration and visualization". bioRxiv. 2024. DOI: 10.1101/2024.11.26.625339.

Contributors

• Primary developer and GitHub maintainer: Nguyen Tran Nam Tien (current)
• Advisor and PI: Seongoh Park, Ph.D. and Nguyen Phuoc Long, M.D., Ph.D.

License

This repository is licensed under the MIT License.