PPTC PDX Oncoprint Generation

Authors:	Jo Lynne Rokita Alvin Farrel Khushbu Patel
Contact:	Jo Lynne Rokita (rokita@email.chop.edu)
Organization:	CHOP
Status:	Complete
Date:	2025-01-14

Introduction

Here, we provide scripts to enable reproducible generation of Manuscript Figure 2: oncoprints by PDX histology and Figure 3: co-oncoplots for diagnosis/relapse samples in neuroblastoma, BCP-ALL, T-ALL, and osteosarcoma. This repo contains code for:

1. Create expanded oncoprint matrices used to reproduces Figure 2 and 3

Details

• RUN-create-full-oncoprint-revision.R
• load-maf-maftools.R
• cluster-scores.R
• merge-mut-CN-fusion-matrices.R
• co-oncoplots.R
• merge-mut-CN-matrices.R
• create-CN-matrices.R
• mutation-color-function.R
• create-complexheat-oncoprint-revision.R
• reformat-CN-matrix-to-df.R
• create-mut-matrices.R
• reformat-clinical.R
• create-mut-sigs-matrix.R
• reformat-fusion-as-matrix.R
• demog-color-function.R
• reformat-fusion-for-maf-revision.R
• install-packages.R

Software Requirements

R 3.4.3

Pipeline

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

# Run script to create pie chart
Rscript ~/create-pptc-pdx-oncoprints/R/RUN-create-full-oncoprint-revision.R

Results

Results will appear in the onco-out folder