PPTC TMB Plots

Authors:	Jo Lynne Rokita
Contact:	Jo Lynne Rokita (rokita@email.chop.edu)
Organization:	CHOP
Status:	In-process
Date:	2024-09-29

Introduction

Here, we provide scripts to enable reproducible generation of Manuscript Figures 2B and S3B: TMB plots for diagnosis/relapse samples across the cohort, within neuroblastoma, BCP-ALL, T-ALL, and osteosarcoma, and between paired diagnosis/relapse samples. This repo contains code for:

1. Creating TMB plot (Figure S3B) and TMB violin plots (Figure 3B)
2. Creating summary statistic tables included in Table S4: Ages and TMB by histology

Details

• TMB.R
• demog-color-function.R
• install-packages.R
• theme.R

Software Requirements

R 3.4.3

Pipeline

# How to run:
# Download github repository in your home directory (~/)
git clone https://github.com/marislab/pptc-pdx-tmb.git

# Run script to create pie chart
Rscript ~/pptc-pdx-tmb/R/TMB.R

Results

Results will appear in the results folder