Authors: | Jo Lynne Rokita
Alvin Farrel Khushbu Patel |
---|---|
Contact: | Jo Lynne Rokita (rokita@email.chop.edu) |
Organization: | CHOP |
Status: | Complete |
Date: | 2024-07-17 |
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:
- Create expanded oncoprint matrices used to reproduces Figure 2 and 3
- 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
R 3.4.3
# 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 will appear in the onco-out folder