Scripts to create nice gistic visualisations.
Please excuse the bad coding, and light documentation!
- Developed using perl v5.26.1 built for x86_64-linux-gnu-thread-multi
- Developed using R v3.6.1 built for x86_64-conda_cos6-linux-gnu
- AFAIK no special libraries are required so this should work on any perl v5.x.x and R v3.x.x
First run gistic2.0 (this is tested on the output of gistic 2.0.23)
First create a table that will be used for the plotting script:
perl gistic_2_dataframe_for_plotting.pl scores.gistic del_genes.conf_20.txt amp_genes.conf_20.txt > myProject_gistic_table.tsv
Create the plot:
R -f plot_gistic_table.r --args myProject_gistic_table.tsv
display myProject_gistic_table.tsv.pdf
Create the plot, but adding in other genes that you are interested in (in a 4 column BED file, no chr prefix, and 4th column is the name)
R -f plot_gistic_table.r --args myProject_gistic_table.tsv my_favourite_genes.bed
If you want to change the genes reported by gistic, find the lines with "Gene_amp" and "Gene_del", and modify the column with the gene names
We use SemVer for versioning. For the versions available, see the tags on this repository.
Naveed Ishaque
This project is licensed under the MIT License - see the LICENSE file for details
Dorett I Odoni