Viz Shiny

Local Shiny app starter with machine-specific settings separated from app code.

First-time setup

Install the required R packages:

source("install_packages.R")

Copy .Renviron.example to .Renviron if you want local machine overrides:

file.copy(".Renviron.example", ".Renviron", overwrite = FALSE)

Run the app from this folder:

source("run_local.R")

By default, the app runs locally at:

http://127.0.0.1:3838

Use Choose Seurat RDS file to select and load a file visible to the computer running the app. The app reads that Seurat .rds file from disk; it does not upload the file through the browser. Users can choose sample, cell type, and comparison metadata columns, set comparison-group colors, enter one or more genes, view sample-by-cell-type pseudobulk expression plots with mean crossbars and Wilcoxon statistics, and download expression plots as png, pdf, or svg.

Files

• app.R: the Shiny application.
• R/visualization.R: pseudobulk aggregation, plotting, and Wilcoxon statistics helpers.
• config.yml: app settings, with separate sections such as default and local.
• .Rprofile: local R startup options for Shiny host, port, and active config.
• .Renviron.example: template for local environment variables and secrets.
• .Renviron.server.example: template used when the app runs under Shiny Server.
• install_packages.R: installs required R packages if they are missing.
• run_local.R: starts the app with the local configuration.
• viz_shiny.Rproj: RStudio project file for opening this folder as the project root.
• .gitignore: keeps local data, output, logs, and secrets out of version control.