CHICO Shiny App

Interactive Shiny application for the CHICO study, combining cohort background, participant summaries, and microbiome comparison in an editorial-style interface.

Highlights

• About: study background, cohort context, and manuscript-style overview
• Data Information: participant summaries from sample_info_genus
• Data Visualization: interactive taxon comparison and Top-N composition view
• Authors: contributor and institutional information

Install

remotes::install_github("jaspershen-lab/chico_shiny")

Run

library(chicoshiny)
run_chico_shiny()

Run From Source

Recommended from the repository root:

devtools::load_all()
run_chico_shiny()

Manual loading also works:

source("R/utils_paths.R")
source("R/app_ui.R")
source("R/app_server.R")
source("R/run_app.R")
run_chico_shiny()

Visualization Modes

Single Taxon Distribution

Compare one selected taxon across one or more groups.

• controls: Level, Bacteria, Group type, Group
• output: interactive boxplot with jittered points
• hover: sample_id, group, abundance
• statistics:
  • two groups: Wilcoxon rank-sum test
  • more than two groups: Kruskal-Wallis test

Top-N Taxa Stacked Bar

Compare compositional patterns across selected groups.

• controls: Level, Top N taxa, Group type, Group
• supports two or more groups
• collapses remaining taxa into Others
• returns a per-group compositional summary table

Data Information Page

Built from sample_info_genus.

Summary page includes:

• age distribution
• Affect pie chart
• risk pie chart
• persistent pie chart

Participant table includes these columns when available:

• sample_id
• Age
• Affect
• virus
• virus_number
• risk
• persistent

Deployment Notes

The app depends on packaged resources under inst/:

• inst/data/
• inst/www/
• inst/markdown/

When deploying to a server, make sure the full project directory is included. Missing inst/ resources will cause missing images, markdown content, or datasets.

Troubleshooting

Couldn't normalize path in addResourcePath

Usually caused by running from source without loading the project correctly.

Use:

devtools::load_all()
run_chico_shiny()

from the repository root.

Browser tab shows HTML like <div class="...">

This comes from an invalid page title being rendered as HTML text. Redeploy the latest version and hard refresh the browser.

Project Files

• R/app_ui.R: UI
• R/app_server.R: server logic
• R/run_app.R: launcher
• R/utils_paths.R: local/package path helpers
• inst/markdown/about.html: About page content
• inst/markdown/authors.html: Authors page content

Entry Point

run_chico_shiny()