OpenPedCan-exprs-shinyapp

Authors:	Komal S Rathi
Contact:	[email protected]
Organization:	D3B, CHOP
Status:	This is "work in progress"
Date:	2024-11-13

Introduction

Mock app built using R shiny to create tumor vs normal and pan-cancer plots to visualize TPM expression.

Structure

.
    ├── R
    │   ├── pubTheme.R
    │   ├── pan_cancer_plot.R
    │   ├── tumor_vs_normal_plot.R
    │   └── viewDataTable.R
    ├── README.rst
    ├── data
    │   ├── efo-mondo-map.tsv
    │   ├── ensg-hugo-rmtl-mapping.tsv
    │   ├── gene-expression-rsem-tpm-collapsed.rds
    │   └── histologies.tsv
    ├── server.R
    ├── ui.R
    └── www

Functions:

1. R/viewDataTable.R: DT::datatable with various add-on, buttons etc
2. R/pubTheme.R: ggplot2 publication quality themes
3. R/pan_cancer_plot.R: function for pan-cancer plots
4. R/tumor_vs_normal_plot.R: function for tumor vs normal plots

Input:

Input files used are:

1. Expression matrix: data/gene-expression-rsem-tpm-collapsed.rds
2. Histologies file: data/histologies.tsv
3. EFO MONDO mapping file: data/efo-mondo-map.tsv
4. Ensembl ID and RMTL mapping file: data/ensg-hugo-rmtl-mapping.tsv

The input files can be downloaded by cloning this repo and running the download script: https://github.com/PediatricOpenTargets/OpenPedCan-analysis

Output:

Two types of output created using this app: one is dynamic (which can be seen on the app as plotly plots and DT tables) and the corresponding static version is written to the www/ folder as .png and .tsv files.

Note: data/ (input directory) and www/ (output directory) have been added to .gitignore.