CycleViz examples

Simple - GBM39 ecDNA

Data derived from GBM39 glioblastoma cell line published in Turner et al., https://pubmed.ncbi.nlm.nih.gov/28178237/

This simple example does not use a YAML file to specify plot parameters.

1. Enter GBM39 example directory

cd $CV_SRC/examples/GBM39

2. Call CycleViz

$CV_SRC/CycleViz.py --ref hg19 --cycles_file FF-4_amplicon1_cycles.txt --cycle 1 -g FF-4_amplicon1_graph.txt --rotate_to_min --figure_size_style small

Recall from the documentation that --figure_size_style small rescales the image to enable better sizing of the image at reduced scales.

Complex - T41 ecDNA

Data derived from oropharyngeal squamous cell carinoma with hybrid human-viral ecDNA from Pang et al., https://pubmed.ncbi.nlm.nih.gov/34548317/

1. Enter the T41 example directory

cd $CV_SRC/examples/T41

2. Call CycleViz

Note that the order in which the feature YAML files are provided specifies the order in which the interior tracks appear (first is innermost, last is outermost).

$CV_SRC/CycleViz.py --input_yaml_file t41_CV.yaml --feature_yaml_list T41_link_track.yaml T41_wgs_track.yaml T41_rna_track.yaml