folder_structure_documentation.md

Web Application Folder Structure Documentation

This document outlines the required folder structure for the TaijiChat R Shiny application, primarily focusing on the www/ directory, which houses data files and static assets like images.

Root Directory Structure

The application's root directory contains the core R scripts and the www/ directory:

/
|-- server.R
|-- ui.R
|-- www/
|-- (other development files like .git/, codebase_analysis.md etc.)

www/ Directory Structure

The www/ directory is crucial as Shiny automatically makes its contents accessible to the web browser. It needs to be organized as follows for the application to find its resources:

www/
|-- tablePagerank/                 # Excel files for TF PageRank scores
|   |-- Table_TF PageRank Scores for Audrey.xlsx # Contains table(s) with PageRank scores for Transcription Factors (TFs), potentially a master or specific analysis file.
|   |-- Naive.xlsx                 # TF data related to Naive cell state.
|   |-- TE.xlsx                    # TF data related to T Exhausted cell state.
|   |-- MP.xlsx                    # TF data related to Memory Precursor cell state.
|   |-- TCM.xlsx                   # TF data related to Central Memory T cell state.
|   |-- TEM.xlsx                   # TF data related to Effector Memory T cell state.
|   |-- TRM.xlsx                   # TF data related to Resident Memory T cell state.
|   |-- TEXprog.xlsx               # TF data related to Progenitor Exhausted T cell state.
|   |-- TEXeff.xlsx                # TF data related to Effector Exhausted T cell state.
|   |-- TEXterm.xlsx               # TF data related to Terminally Exhausted T cell state.
|
|-- waveanalysis/                  # Assets for TF Wave Analysis
|   |-- searchtfwaves.xlsx         # Contains TF names organized by different "waves" of activity or expression.
|   |-- tfwaveanal.png             # Overview image
|   |-- c1.jpg                     # Wave 1 image
|   |-- c2.jpg                     # Wave 2 image
|   |-- c3.jpg                     # Wave 3 image
|   |-- c4.jpg                     # Wave 4 image
|   |-- c5.jpg                     # Wave 5 image
|   |-- c6.jpg                     # Wave 6 image
|   |-- c7.jpg                     # Wave 7 image
|   |-- c1_selected_GO_KEGG.jpg
|   |-- c2_selected_GO_KEGG_v2.jpg
|   |-- c3_selected_GO_KEGG.jpg
|   |-- c4_selected_GO_KEGG.jpg
|   |-- c5_selected_GO_KEGG.jpg 
|   |-- c6_selected_GO_KEGG.jpg
|   |-- c7_selected_GO_KEGG.jpg
|   |
|   |-- txtJPG/                    # "Ranked Text" images for Wave Analysis
|       |-- c1_ranked_1.jpg
|       |-- c1_ranked_2.jpg
|       |-- c2_ranked.jpg
|       |-- c3_ranked.jpg
|       |-- c4_ranked.jpg
|       |-- c5_ranked.jpg
|       |-- c6_ranked.jpg
|       |-- c7_ranked.jpg
|
|-- TFcorintextrm/                 # Data for TF-TF correlation
|   |-- TF-TFcorTRMTEX.xlsx        # Contains data on correlations between Transcription Factors, possibly focused on TRM and TEX states.
|
|-- tfcommunities/                 # Data for TF communities
|   |-- trmcommunities.xlsx        # Data defining TF communities within the TRM (Resident Memory T cell) state.
|   |-- texcommunities.xlsx        # Data defining TF communities within TEX (Exhausted T cell) states.
|
|-- bubbleplots/                   # Images for cell-state specific bubble plots
|   |-- naivebubble.jpg
|   |-- tebubble.jpg
|   |-- mpbubble.jpg
|   |-- tcmbubble.jpg
|   |-- tembubble.jpg
|   |-- trmbubble.jpg
|   |-- texprogbubble.jpg
|   |-- texintbubble.jpg           # (Used for TEXeff-like)
|   |-- textermbubble.jpg
|
|-- tfcat/                         # Images for the TF Catalog section
|   |-- onlycellstates.png
|   |-- multistatesheatmap.png
|
|-- networkanalysis/               # Images for TF Network Analysis section
|   |-- tfcorrdesc.png
|   |-- community.jpg
|   |-- trmtexcom.png
|   |-- tfcompathway.png
|
|-- multi-omicsdata.xlsx           # Main multi-omics data file (e.g., gene expression, chromatin accessibility, protein levels). Structure needs to be inferred or predefined for agent use.
|
|-- homedesc.png                   # Image for the home page
|-- ucsdlogo.png                   # UCSD Logo
|-- salklogo.png                   # Salk Logo
|-- unclogo.jpg                    # UNC Logo
|-- csdescrip.jpeg                 # Image for the modal dialog (if used)

Notes:

• The filenames listed are based on the explicit references in server.R and ui.R.
• This structure primarily covers files loaded directly by the R scripts or referenced in UI image tags.
• For the application to be fully functional, all listed Excel files and image assets must be present in these locations with the correct names.
• If an Excel file (e.g., for individual cell states) is derived from a single source table, it's assumed that the source table has been appropriately processed or split into these individual files, or that the application can handle the single source if the server-side logic were adapted.

This documentation should help in setting up the necessary file environment for the application.